DCGL v2.0: An R Package for Unveiling Differential Regulation from Differential Co-expression
Differential co-expression analysis (DCEA) has emerged in recent years as a novel, systematic investigation into gene expression data. While most DCEA studies or tools focus on the co-expression relationships among genes, some are developing a potentially more promising research domain, differential...
Uložené v:
| Vydané v: | PloS one Ročník 8; číslo 11; s. e79729 |
|---|---|
| Hlavní autori: | , , , , , , , |
| Médium: | Journal Article |
| Jazyk: | English |
| Vydavateľské údaje: |
United States
Public Library of Science
20.11.2013
Public Library of Science (PLoS) |
| Predmet: | |
| ISSN: | 1932-6203, 1932-6203 |
| On-line prístup: | Získať plný text |
| Tagy: |
Pridať tag
Žiadne tagy, Buďte prvý, kto otaguje tento záznam!
|
| Abstract | Differential co-expression analysis (DCEA) has emerged in recent years as a novel, systematic investigation into gene expression data. While most DCEA studies or tools focus on the co-expression relationships among genes, some are developing a potentially more promising research domain, differential regulation analysis (DRA). In our previously proposed R package DCGL v1.0, we provided functions to facilitate basic differential co-expression analyses; however, the output from DCGL v1.0 could not be translated into differential regulation mechanisms in a straightforward manner.
To advance from DCEA to DRA, we upgraded the DCGL package from v1.0 to v2.0. A new module named "Differential Regulation Analysis" (DRA) was designed, which consists of three major functions: DRsort, DRplot, and DRrank. DRsort selects differentially regulated genes (DRGs) and differentially regulated links (DRLs) according to the transcription factor (TF)-to-target information. DRrank prioritizes the TFs in terms of their potential relevance to the phenotype of interest. DRplot graphically visualizes differentially co-expressed links (DCLs) and/or TF-to-target links in a network context. In addition to these new modules, we streamlined the codes from v1.0. The evaluation results proved that our differential regulation analysis is able to capture the regulators relevant to the biological subject.
With ample functions to facilitate differential regulation analysis, DCGL v2.0 was upgraded from a DCEA tool to a DRA tool, which may unveil the underlying differential regulation from the observed differential co-expression. DCGL v2.0 can be applied to a wide range of gene expression data in order to systematically identify novel regulators that have not yet been documented as critical.
DCGL v2.0 package is available at http://cran.r-project.org/web/packages/DCGL/index.html or at our project home page http://lifecenter.sgst.cn/main/en/dcgl.jsp. |
|---|---|
| AbstractList | Motivation To advance from DCEA to DRA, we upgraded the DCGL package from v1.0 to v2.0. A new module named "Differential Regulation Analysis" (DRA) was designed, which consists of three major functions: DRsort, DRplot, and DRrank. DRsort selects differentially regulated genes (DRGs) and differentially regulated links (DRLs) according to the transcription factor (TF)-to-target information. DRrank prioritizes the TFs in terms of their potential relevance to the phenotype of interest. DRplot graphically visualizes differentially co-expressed links (DCLs) and/or TF-to-target links in a network context. In addition to these new modules, we streamlined the codes from v1.0. The evaluation results proved that our differential regulation analysis is able to capture the regulators relevant to the biological subject. With ample functions to facilitate differential regulation analysis, DCGL v2.0 was upgraded from a DCEA tool to a DRA tool, which may unveil the underlying differential regulation from the observed differential co-expression. DCGL v2.0 can be applied to a wide range of gene expression data in order to systematically identify novel regulators that have not yet been documented as critical. Differential co-expression analysis (DCEA) has emerged in recent years as a novel, systematic investigation into gene expression data. While most DCEA studies or tools focus on the co-expression relationships among genes, some are developing a potentially more promising research domain, differential regulation analysis (DRA). In our previously proposed R package DCGL v1.0, we provided functions to facilitate basic differential co-expression analyses; however, the output from DCGL v1.0 could not be translated into differential regulation mechanisms in a straightforward manner.To advance from DCEA to DRA, we upgraded the DCGL package from v1.0 to v2.0. A new module named "Differential Regulation Analysis" (DRA) was designed, which consists of three major functions: DRsort, DRplot, and DRrank. DRsort selects differentially regulated genes (DRGs) and differentially regulated links (DRLs) according to the transcription factor (TF)-to-target information. DRrank prioritizes the TFs in terms of their potential relevance to the phenotype of interest. DRplot graphically visualizes differentially co-expressed links (DCLs) and/or TF-to-target links in a network context. In addition to these new modules, we streamlined the codes from v1.0. The evaluation results proved that our differential regulation analysis is able to capture the regulators relevant to the biological subject.With ample functions to facilitate differential regulation analysis, DCGL v2.0 was upgraded from a DCEA tool to a DRA tool, which may unveil the underlying differential regulation from the observed differential co-expression. DCGL v2.0 can be applied to a wide range of gene expression data in order to systematically identify novel regulators that have not yet been documented as critical.DCGL v2.0 package is available at http://cran.r-project.org/web/packages/DCGL/index.html or at our project home page http://lifecenter.sgst.cn/main/en/dcgl.jsp. Differential co-expression analysis (DCEA) has emerged in recent years as a novel, systematic investigation into gene expression data. While most DCEA studies or tools focus on the co-expression relationships among genes, some are developing a potentially more promising research domain, differential regulation analysis (DRA). In our previously proposed R package DCGL v1.0, we provided functions to facilitate basic differential co-expression analyses; however, the output from DCGL v1.0 could not be translated into differential regulation mechanisms in a straightforward manner.MOTIVATIONDifferential co-expression analysis (DCEA) has emerged in recent years as a novel, systematic investigation into gene expression data. While most DCEA studies or tools focus on the co-expression relationships among genes, some are developing a potentially more promising research domain, differential regulation analysis (DRA). In our previously proposed R package DCGL v1.0, we provided functions to facilitate basic differential co-expression analyses; however, the output from DCGL v1.0 could not be translated into differential regulation mechanisms in a straightforward manner.To advance from DCEA to DRA, we upgraded the DCGL package from v1.0 to v2.0. A new module named "Differential Regulation Analysis" (DRA) was designed, which consists of three major functions: DRsort, DRplot, and DRrank. DRsort selects differentially regulated genes (DRGs) and differentially regulated links (DRLs) according to the transcription factor (TF)-to-target information. DRrank prioritizes the TFs in terms of their potential relevance to the phenotype of interest. DRplot graphically visualizes differentially co-expressed links (DCLs) and/or TF-to-target links in a network context. In addition to these new modules, we streamlined the codes from v1.0. The evaluation results proved that our differential regulation analysis is able to capture the regulators relevant to the biological subject.RESULTSTo advance from DCEA to DRA, we upgraded the DCGL package from v1.0 to v2.0. A new module named "Differential Regulation Analysis" (DRA) was designed, which consists of three major functions: DRsort, DRplot, and DRrank. DRsort selects differentially regulated genes (DRGs) and differentially regulated links (DRLs) according to the transcription factor (TF)-to-target information. DRrank prioritizes the TFs in terms of their potential relevance to the phenotype of interest. DRplot graphically visualizes differentially co-expressed links (DCLs) and/or TF-to-target links in a network context. In addition to these new modules, we streamlined the codes from v1.0. The evaluation results proved that our differential regulation analysis is able to capture the regulators relevant to the biological subject.With ample functions to facilitate differential regulation analysis, DCGL v2.0 was upgraded from a DCEA tool to a DRA tool, which may unveil the underlying differential regulation from the observed differential co-expression. DCGL v2.0 can be applied to a wide range of gene expression data in order to systematically identify novel regulators that have not yet been documented as critical.CONCLUSIONSWith ample functions to facilitate differential regulation analysis, DCGL v2.0 was upgraded from a DCEA tool to a DRA tool, which may unveil the underlying differential regulation from the observed differential co-expression. DCGL v2.0 can be applied to a wide range of gene expression data in order to systematically identify novel regulators that have not yet been documented as critical.DCGL v2.0 package is available at http://cran.r-project.org/web/packages/DCGL/index.html or at our project home page http://lifecenter.sgst.cn/main/en/dcgl.jsp.AVAILABILITYDCGL v2.0 package is available at http://cran.r-project.org/web/packages/DCGL/index.html or at our project home page http://lifecenter.sgst.cn/main/en/dcgl.jsp. Motivation Differential co-expression analysis (DCEA) has emerged in recent years as a novel, systematic investigation into gene expression data. While most DCEA studies or tools focus on the co-expression relationships among genes, some are developing a potentially more promising research domain, differential regulation analysis (DRA). In our previously proposed R package DCGL v1.0, we provided functions to facilitate basic differential co-expression analyses; however, the output from DCGL v1.0 could not be translated into differential regulation mechanisms in a straightforward manner. Results To advance from DCEA to DRA, we upgraded the DCGL package from v1.0 to v2.0. A new module named “Differential Regulation Analysis” (DRA) was designed, which consists of three major functions: DRsort, DRplot, and DRrank. DRsort selects differentially regulated genes (DRGs) and differentially regulated links (DRLs) according to the transcription factor (TF)-to-target information. DRrank prioritizes the TFs in terms of their potential relevance to the phenotype of interest. DRplot graphically visualizes differentially co-expressed links (DCLs) and/or TF-to-target links in a network context. In addition to these new modules, we streamlined the codes from v1.0. The evaluation results proved that our differential regulation analysis is able to capture the regulators relevant to the biological subject. Conclusions With ample functions to facilitate differential regulation analysis, DCGL v2.0 was upgraded from a DCEA tool to a DRA tool, which may unveil the underlying differential regulation from the observed differential co-expression. DCGL v2.0 can be applied to a wide range of gene expression data in order to systematically identify novel regulators that have not yet been documented as critical. Availability DCGL v2.0 package is available at http://cran.r-project.org/web/packages/DCGL/index.html or at our project home page http://lifecenter.sgst.cn/main/en/dcgl.jsp. Differential co-expression analysis (DCEA) has emerged in recent years as a novel, systematic investigation into gene expression data. While most DCEA studies or tools focus on the co-expression relationships among genes, some are developing a potentially more promising research domain, differential regulation analysis (DRA). In our previously proposed R package DCGL v1.0, we provided functions to facilitate basic differential co-expression analyses; however, the output from DCGL v1.0 could not be translated into differential regulation mechanisms in a straightforward manner. To advance from DCEA to DRA, we upgraded the DCGL package from v1.0 to v2.0. A new module named "Differential Regulation Analysis" (DRA) was designed, which consists of three major functions: DRsort, DRplot, and DRrank. DRsort selects differentially regulated genes (DRGs) and differentially regulated links (DRLs) according to the transcription factor (TF)-to-target information. DRrank prioritizes the TFs in terms of their potential relevance to the phenotype of interest. DRplot graphically visualizes differentially co-expressed links (DCLs) and/or TF-to-target links in a network context. In addition to these new modules, we streamlined the codes from v1.0. The evaluation results proved that our differential regulation analysis is able to capture the regulators relevant to the biological subject. With ample functions to facilitate differential regulation analysis, DCGL v2.0 was upgraded from a DCEA tool to a DRA tool, which may unveil the underlying differential regulation from the observed differential co-expression. DCGL v2.0 can be applied to a wide range of gene expression data in order to systematically identify novel regulators that have not yet been documented as critical. DCGL v2.0 package is available at http://cran.r-project.org/web/packages/DCGL/index.html or at our project home page http://lifecenter.sgst.cn/main/en/dcgl.jsp. Motivation Differential co-expression analysis (DCEA) has emerged in recent years as a novel, systematic investigation into gene expression data. While most DCEA studies or tools focus on the co-expression relationships among genes, some are developing a potentially more promising research domain, differential regulation analysis (DRA). In our previously proposed R package DCGL v1.0, we provided functions to facilitate basic differential co-expression analyses; however, the output from DCGL v1.0 could not be translated into differential regulation mechanisms in a straightforward manner. Results To advance from DCEA to DRA, we upgraded the DCGL package from v1.0 to v2.0. A new module named "Differential Regulation Analysis" (DRA) was designed, which consists of three major functions: DRsort, DRplot, and DRrank. DRsort selects differentially regulated genes (DRGs) and differentially regulated links (DRLs) according to the transcription factor (TF)-to-target information. DRrank prioritizes the TFs in terms of their potential relevance to the phenotype of interest. DRplot graphically visualizes differentially co-expressed links (DCLs) and/or TF-to-target links in a network context. In addition to these new modules, we streamlined the codes from v1.0. The evaluation results proved that our differential regulation analysis is able to capture the regulators relevant to the biological subject. Conclusions With ample functions to facilitate differential regulation analysis, DCGL v2.0 was upgraded from a DCEA tool to a DRA tool, which may unveil the underlying differential regulation from the observed differential co-expression. DCGL v2.0 can be applied to a wide range of gene expression data in order to systematically identify novel regulators that have not yet been documented as critical. Availability DCGL v2.0 package is available at Motivation Differential co-expression analysis (DCEA) has emerged in recent years as a novel, systematic investigation into gene expression data. While most DCEA studies or tools focus on the co-expression relationships among genes, some are developing a potentially more promising research domain, differential regulation analysis (DRA). In our previously proposed R package DCGL v1.0, we provided functions to facilitate basic differential co-expression analyses; however, the output from DCGL v1.0 could not be translated into differential regulation mechanisms in a straightforward manner. Results To advance from DCEA to DRA, we upgraded the DCGL package from v1.0 to v2.0. A new module named “Differential Regulation Analysis” (DRA) was designed, which consists of three major functions: DRsort , DRplot , and DRrank . DRsort selects differentially regulated genes (DRGs) and differentially regulated links (DRLs) according to the transcription factor (TF)-to-target information. DRrank prioritizes the TFs in terms of their potential relevance to the phenotype of interest. DRplot graphically visualizes differentially co-expressed links (DCLs) and/or TF-to-target links in a network context. In addition to these new modules, we streamlined the codes from v1.0. The evaluation results proved that our differential regulation analysis is able to capture the regulators relevant to the biological subject. Conclusions With ample functions to facilitate differential regulation analysis, DCGL v2.0 was upgraded from a DCEA tool to a DRA tool, which may unveil the underlying differential regulation from the observed differential co-expression. DCGL v2.0 can be applied to a wide range of gene expression data in order to systematically identify novel regulators that have not yet been documented as critical. Availability DCGL v2.0 package is available at http://cran.r-project.org/web/packages/DCGL/index.html or at our project home page http://lifecenter.sgst.cn/main/en/dcgl.jsp. |
| Audience | Academic |
| Author | Yu, Hui Li, Yuan-Yuan Ma, Liang-Xiao Yang, Jing Zhao, Zhongming Li, Yi-Xue Liu, Lei Liu, Bao-Hong |
| AuthorAffiliation | 4 Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America University of California, Los Angeles, United States of America 1 School of Biotechnology, East China University of Science and Technology, Shanghai, P. R. China 5 Departments of Psychiatry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America 3 Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, P. R. China 2 Bioinformatics Center, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China 6 Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America |
| AuthorAffiliation_xml | – name: 3 Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, P. R. China – name: 2 Bioinformatics Center, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China – name: 5 Departments of Psychiatry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America – name: 1 School of Biotechnology, East China University of Science and Technology, Shanghai, P. R. China – name: 6 Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America – name: University of California, Los Angeles, United States of America – name: 4 Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America |
| Author_xml | – sequence: 1 givenname: Jing surname: Yang fullname: Yang, Jing – sequence: 2 givenname: Hui surname: Yu fullname: Yu, Hui – sequence: 3 givenname: Bao-Hong surname: Liu fullname: Liu, Bao-Hong – sequence: 4 givenname: Zhongming surname: Zhao fullname: Zhao, Zhongming – sequence: 5 givenname: Lei surname: Liu fullname: Liu, Lei – sequence: 6 givenname: Liang-Xiao surname: Ma fullname: Ma, Liang-Xiao – sequence: 7 givenname: Yi-Xue surname: Li fullname: Li, Yi-Xue – sequence: 8 givenname: Yuan-Yuan surname: Li fullname: Li, Yuan-Yuan |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/24278165$$D View this record in MEDLINE/PubMed |
| BookMark | eNqNk11v0zAUhiM0xLbCP0AQaRKCixZ_xUl2gVR1MCpVGiqMO2S5_khd3LjYSTX-PW6XomaaEMpFonOe97XPyTnnyUntapUkLyEYQZzD9yvX-prb0SaGRwDkZY7KJ8kZLDEaUgTwydH3aXIewgqADBeUPktOEUF5AWl2lvy4mlzP0i0agct0XKfz9AsXP3mlUu18eltvlbGmrtIro7Xyqm4Mt-lcVa3ljXF1qr1b95MTN1R3G69CiPnnyVPNbVAvuvcguf308dvk83B2cz2djGdDQUvUDAnksMC4ICLPtAYLSZWkkmggKRKo4DnIpEYSLgq5EEgXguaYcEkJJlmuSowHyet73411gXWdCQwSCiAFeezDIJneE9LxFdt4s-b-N3PcsH3A-Ypx3xhhFVughS6jCkORE6JRWUoc74I4AkRkBEavD91p7WKtpIiVe257pv1MbZascluGC5wVGYkGbzsD7361KjRsbYJQ1vJauXZ_bwQLiugOvXiAPl5dR1U8FmBq7eK5YmfKxiT-6YJinEdq9AgVH6nWRsQx0ibGe4J3PUFkGnXXVLwNgU2_zv-fvfneZ98csUvFbbMMzra7kQp98NVxp_-2-DC_Ebi8B4R3IXilmTDNfjRjacYyCNhuWQ5NY7tlYd2yRDF5ID74_1P2BxYyFgA |
| CitedBy_id | crossref_primary_10_3390_ijms20235988 crossref_primary_10_1016_j_compbiolchem_2020_107317 crossref_primary_10_1186_s12920_020_00772_3 crossref_primary_10_1007_s11427_014_4762_7 crossref_primary_10_1371_journal_pone_0210672 crossref_primary_10_3389_fgene_2015_00312 crossref_primary_10_3389_fgene_2021_680217 crossref_primary_10_1016_j_artmed_2017_02_006 crossref_primary_10_3390_genes9050245 crossref_primary_10_1111_jcmm_15159 crossref_primary_10_1186_s12870_021_02965_z crossref_primary_10_1007_s00404_015_3833_8 crossref_primary_10_1007_s10265_021_01338_9 crossref_primary_10_1093_nar_gkx350 crossref_primary_10_1038_s41438_020_0238_z crossref_primary_10_1155_2016_4241293 crossref_primary_10_3389_fgene_2020_560997 crossref_primary_10_1080_15592294_2019_1634975 crossref_primary_10_1016_j_artmed_2017_01_002 crossref_primary_10_1186_1471_2105_15_S10_P33 crossref_primary_10_1186_s12918_016_0280_5 crossref_primary_10_1371_journal_pone_0141859 crossref_primary_10_3389_fimmu_2021_699633 crossref_primary_10_1186_s10020_022_00468_7 crossref_primary_10_1371_journal_pone_0135831 crossref_primary_10_1096_fj_201903088R crossref_primary_10_1038_srep13295 crossref_primary_10_1038_srep35064 crossref_primary_10_3892_etm_2018_6026 crossref_primary_10_1109_TCBB_2019_2893170 crossref_primary_10_1186_s12859_015_0543_y crossref_primary_10_3390_genes13050862 crossref_primary_10_1093_schbul_sbv170 crossref_primary_10_1016_j_genrep_2022_101688 crossref_primary_10_1186_s12918_018_0564_z crossref_primary_10_1111_sji_12345 crossref_primary_10_1155_2017_8347085 crossref_primary_10_1186_s12859_020_3468_z crossref_primary_10_2217_fon_2019_0275 crossref_primary_10_3389_fcell_2021_801687 crossref_primary_10_3389_fimmu_2025_1575490 crossref_primary_10_1186_s12918_016_0315_y crossref_primary_10_3390_ijms21249461 crossref_primary_10_3389_fpls_2021_744654 crossref_primary_10_3389_fpls_2021_640746 crossref_primary_10_1186_s12920_020_00761_6 crossref_primary_10_3390_genes12050665 crossref_primary_10_1016_j_clinre_2015_04_005 crossref_primary_10_3892_ol_2017_6267 crossref_primary_10_1093_pcp_pcy044 crossref_primary_10_1097_MD_0000000000027428 crossref_primary_10_1186_1756_0500_7_886 crossref_primary_10_3892_mmr_2017_8213 crossref_primary_10_1186_s13000_014_0210_z crossref_primary_10_1186_s13062_015_0088_z crossref_primary_10_1038_s41598_020_61633_8 crossref_primary_10_1371_journal_pone_0240523 |
| Cites_doi | 10.1093/bioinformatics/bti722 10.1093/nar/gkq149 10.1038/30918 10.1007/s10067-012-2143-9 10.3748/wjg.v8.i2.203 10.1093/bioinformatics/btl392 10.2202/1544-6115.1027 10.1210/en.2008-0563 10.1186/1471-2105-7-509 10.1371/journal.pcbi.1000382 10.1093/bioinformatics/bti1120 10.1186/1471-2105-7-12 10.1016/j.tig.2010.05.001 10.1016/j.gpb.2012.08.003 10.1093/nar/gkr130 10.1371/journal.pone.0003911 10.1373/clinchem.2007.089144 10.1371/journal.pone.0052319 10.1186/1471-2105-11-S11-S5 10.1371/journal.pone.0016916 10.6061/clinics/2013(02)OA17 10.1093/bioinformatics/btq051 10.1093/bioinformatics/btm309 10.1186/1471-2105-12-315 10.1016/j.bbrc.2008.12.180 10.1039/c2mb25434d 10.1093/bioinformatics/btp502 10.1016/j.gene.2012.11.028 10.1053/j.gastro.2009.08.005 10.1186/1471-2164-10-327 10.1093/bioinformatics/btq471 10.1007/s11033-012-2449-3 10.1038/nprot.2008.211 10.1158/1055-9965.EPI-09-0767 |
| ContentType | Journal Article |
| Copyright | COPYRIGHT 2013 Public Library of Science 2013 Yang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/3.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2013 Yang et al 2013 Yang et al |
| Copyright_xml | – notice: COPYRIGHT 2013 Public Library of Science – notice: 2013 Yang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/3.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. – notice: 2013 Yang et al 2013 Yang et al |
| DBID | AAYXX CITATION CGR CUY CVF ECM EIF NPM IOV ISR 3V. 7QG 7QL 7QO 7RV 7SN 7SS 7T5 7TG 7TM 7U9 7X2 7X7 7XB 88E 8AO 8C1 8FD 8FE 8FG 8FH 8FI 8FJ 8FK ABJCF ABUWG AEUYN AFKRA ARAPS ATCPS AZQEC BBNVY BENPR BGLVJ BHPHI C1K CCPQU D1I DWQXO FR3 FYUFA GHDGH GNUQQ H94 HCIFZ K9. KB. KB0 KL. L6V LK8 M0K M0S M1P M7N M7P M7S NAPCQ P5Z P62 P64 PATMY PDBOC PHGZM PHGZT PIMPY PJZUB PKEHL PPXIY PQEST PQGLB PQQKQ PQUKI PRINS PTHSS PYCSY RC3 7X8 5PM DOA |
| DOI | 10.1371/journal.pone.0079729 |
| DatabaseName | CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed Gale In Context: Opposing Viewpoints Gale In Context: Science ProQuest Central (Corporate) Animal Behavior Abstracts Bacteriology Abstracts (Microbiology B) Biotechnology Research Abstracts Nursing & Allied Health Database Ecology Abstracts Entomology Abstracts (Full archive) Immunology Abstracts Meteorological & Geoastrophysical Abstracts Nucleic Acids Abstracts Virology and AIDS Abstracts Agricultural Science Collection Health & Medical Collection ProQuest Central (purchase pre-March 2016) Medical Database (Alumni Edition) ProQuest Pharma Collection Public Health Database Technology Research Database ProQuest SciTech Collection ProQuest Technology Collection ProQuest Natural Science Collection Hospital Premium Collection Hospital Premium Collection (Alumni Edition) ProQuest Central (Alumni) (purchase pre-March 2016) Materials Science & Engineering Collection ProQuest Central (Alumni) ProQuest One Sustainability ProQuest Central UK/Ireland ProQuest SciTech Premium Collection Technology Collection Advanced Technologies & Aerospace Collection Agricultural & Environmental Science Collection ProQuest Central Essentials - QC ProQuest SciTech Premium Collection Natural Science Collection Biological Science Collection ProQuest Central ProQuest Technology Collection Natural Science Collection Environmental Sciences and Pollution Management ProQuest One ProQuest Materials Science Collection ProQuest Central Engineering Research Database Health Research Premium Collection Health Research Premium Collection (Alumni) ProQuest Central Student AIDS and Cancer Research Abstracts SciTech Premium Collection ProQuest Health & Medical Complete (Alumni) Materials Science Database Nursing & Allied Health Database (Alumni Edition) Meteorological & Geoastrophysical Abstracts - Academic ProQuest Engineering Collection ProQuest Biological Science Collection Agricultural Science Database ProQuest Health & Medical Collection Medical Database Algology Mycology and Protozoology Abstracts (Microbiology C) Biological Science Database Engineering Database Nursing & Allied Health Premium Advanced Technologies & Aerospace Database ProQuest Advanced Technologies & Aerospace Collection Biotechnology and BioEngineering Abstracts Environmental Science Database Materials Science Collection ProQuest One Academic ProQuest One Academic ProQuest Publicly Available Content Database ProQuest Health & Medical Research Collection ProQuest One Academic Middle East (New) ProQuest One Health & Nursing ProQuest One Academic Eastern Edition (DO NOT USE) ProQuest One Applied & Life Sciences ProQuest One Academic (retired) ProQuest One Academic UKI Edition ProQuest Central China Engineering Collection Environmental Science Collection Genetics Abstracts MEDLINE - Academic PubMed Central (Full Participant titles) DOAJ Directory of Open Access Journals |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) Agricultural Science Database Publicly Available Content Database ProQuest Central Student ProQuest Advanced Technologies & Aerospace Collection ProQuest Central Essentials Nucleic Acids Abstracts SciTech Premium Collection ProQuest Central China Environmental Sciences and Pollution Management ProQuest One Applied & Life Sciences ProQuest One Sustainability Health Research Premium Collection Meteorological & Geoastrophysical Abstracts Natural Science Collection Health & Medical Research Collection Biological Science Collection ProQuest Central (New) ProQuest Medical Library (Alumni) Engineering Collection Advanced Technologies & Aerospace Collection Engineering Database Virology and AIDS Abstracts ProQuest Biological Science Collection ProQuest One Academic Eastern Edition Agricultural Science Collection ProQuest Hospital Collection ProQuest Technology Collection Health Research Premium Collection (Alumni) Biological Science Database Ecology Abstracts ProQuest Hospital Collection (Alumni) Biotechnology and BioEngineering Abstracts Environmental Science Collection Entomology Abstracts Nursing & Allied Health Premium ProQuest Health & Medical Complete ProQuest One Academic UKI Edition Environmental Science Database ProQuest Nursing & Allied Health Source (Alumni) Engineering Research Database ProQuest One Academic Meteorological & Geoastrophysical Abstracts - Academic ProQuest One Academic (New) Technology Collection Technology Research Database ProQuest One Academic Middle East (New) Materials Science Collection ProQuest Health & Medical Complete (Alumni) ProQuest Central (Alumni Edition) ProQuest One Community College ProQuest One Health & Nursing ProQuest Natural Science Collection ProQuest Pharma Collection ProQuest Central ProQuest Health & Medical Research Collection Genetics Abstracts ProQuest Engineering Collection Biotechnology Research Abstracts Health and Medicine Complete (Alumni Edition) ProQuest Central Korea Bacteriology Abstracts (Microbiology B) Algology Mycology and Protozoology Abstracts (Microbiology C) Agricultural & Environmental Science Collection AIDS and Cancer Research Abstracts Materials Science Database ProQuest Materials Science Collection ProQuest Public Health ProQuest Nursing & Allied Health Source ProQuest SciTech Collection Advanced Technologies & Aerospace Database ProQuest Medical Library Animal Behavior Abstracts Materials Science & Engineering Collection Immunology Abstracts ProQuest Central (Alumni) MEDLINE - Academic |
| DatabaseTitleList | MEDLINE - Academic Agricultural Science Database MEDLINE |
| Database_xml | – sequence: 1 dbid: DOA name: Directory of Open Access Journals url: https://www.doaj.org/ sourceTypes: Open Website – sequence: 2 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 3 dbid: PIMPY name: Publicly Available Content Database url: http://search.proquest.com/publiccontent sourceTypes: Aggregation Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Sciences (General) Medicine Biology |
| DocumentTitleAlternate | DCGL v2.0 for Differential Regulation Analysis |
| EISSN | 1932-6203 |
| ExternalDocumentID | 1460160719 oai_doaj_org_article_b2bf960731c744f299d34f02a204c541 PMC3835854 3132456371 A478186337 24278165 10_1371_journal_pone_0079729 |
| Genre | Research Support, Non-U.S. Gov't Journal Article Research Support, N.I.H., Extramural |
| GeographicLocations | United States--US Tennessee Nashville Tennessee |
| GeographicLocations_xml | – name: Nashville Tennessee – name: Tennessee – name: United States--US |
| GrantInformation_xml | – fundername: NCI NIH HHS grantid: R03CA167695 – fundername: NIDCR NIH HHS grantid: R03DE022093 – fundername: NIDCR NIH HHS grantid: R03 DE022093 – fundername: NLM NIH HHS grantid: R01 LM011177 – fundername: NCI NIH HHS grantid: R03 CA167695 – fundername: NLM NIH HHS grantid: R01LM011177 |
| GroupedDBID | --- 123 29O 2WC 53G 5VS 7RV 7X2 7X7 7XC 88E 8AO 8C1 8CJ 8FE 8FG 8FH 8FI 8FJ A8Z AAFWJ AAUCC AAWOE AAYXX ABDBF ABIVO ABJCF ABUWG ACCTH ACGFO ACIHN ACIWK ACPRK ACUHS ADBBV ADRAZ AEAQA AENEX AEUYN AFFHD AFKRA AFPKN AFRAH AHMBA ALMA_UNASSIGNED_HOLDINGS AOIJS APEBS ARAPS ATCPS BAWUL BBNVY BCNDV BENPR BGLVJ BHPHI BKEYQ BPHCQ BVXVI BWKFM CCPQU CITATION CS3 D1I D1J D1K DIK DU5 E3Z EAP EAS EBD EMOBN ESX EX3 F5P FPL FYUFA GROUPED_DOAJ GX1 HCIFZ HH5 HMCUK HYE IAO IEA IGS IHR IHW INH INR IOV IPNFZ IPY ISE ISR ITC K6- KB. KQ8 L6V LK5 LK8 M0K M1P M48 M7P M7R M7S M~E NAPCQ O5R O5S OK1 OVT P2P P62 PATMY PDBOC PHGZM PHGZT PIMPY PJZUB PPXIY PQGLB PQQKQ PROAC PSQYO PTHSS PYCSY RIG RNS RPM SV3 TR2 UKHRP WOQ WOW ~02 ~KM ALIPV CGR CUY CVF ECM EIF NPM PV9 RZL BBORY 3V. 7QG 7QL 7QO 7SN 7SS 7T5 7TG 7TM 7U9 7XB 8FD 8FK AZQEC C1K DWQXO ESTFP FR3 GNUQQ H94 K9. KL. M7N P64 PKEHL PQEST PQUKI PRINS RC3 7X8 PUEGO 5PM - 02 AAPBV ABPTK ADACO BBAFP KM |
| ID | FETCH-LOGICAL-c692t-41a183384c75ff0bd6ed6d4f0d62c28a705df2d1b8dbc2f8c6734ad643457e933 |
| IEDL.DBID | M7P |
| ISICitedReferencesCount | 76 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000327313100041&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| ISSN | 1932-6203 |
| IngestDate | Fri Nov 26 17:12:28 EST 2021 Tue Oct 14 18:57:00 EDT 2025 Tue Nov 04 02:01:35 EST 2025 Mon Sep 08 03:28:37 EDT 2025 Tue Oct 07 07:08:30 EDT 2025 Sat Nov 29 13:32:21 EST 2025 Sat Nov 29 09:55:34 EST 2025 Wed Nov 26 09:21:57 EST 2025 Wed Nov 26 10:41:50 EST 2025 Thu May 22 21:17:37 EDT 2025 Tue Aug 05 11:42:01 EDT 2025 Tue Nov 18 21:43:16 EST 2025 Sat Nov 29 03:33:23 EST 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 11 |
| Language | English |
| License | This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. Creative Commons Attribution License |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c692t-41a183384c75ff0bd6ed6d4f0d62c28a705df2d1b8dbc2f8c6734ad643457e933 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Conceived and designed the experiments: YYL HY JY YXL. Performed the experiments: JY HY BHL. Analyzed the data: JY HY. Contributed reagents/materials/analysis tools: YYL JY HY LXM LL. Wrote the paper: YYL HY JY ZZ. Competing Interests: The authors have declared that no competing interests exist. |
| OpenAccessLink | https://www.proquest.com/docview/1460160719?pq-origsite=%requestingapplication% |
| PMID | 24278165 |
| PQID | 1460160719 |
| PQPubID | 1436336 |
| PageCount | e79729 |
| ParticipantIDs | plos_journals_1460160719 doaj_primary_oai_doaj_org_article_b2bf960731c744f299d34f02a204c541 pubmedcentral_primary_oai_pubmedcentral_nih_gov_3835854 proquest_miscellaneous_1462186264 proquest_journals_1460160719 gale_infotracmisc_A478186337 gale_infotracacademiconefile_A478186337 gale_incontextgauss_ISR_A478186337 gale_incontextgauss_IOV_A478186337 gale_healthsolutions_A478186337 pubmed_primary_24278165 crossref_citationtrail_10_1371_journal_pone_0079729 crossref_primary_10_1371_journal_pone_0079729 |
| PublicationCentury | 2000 |
| PublicationDate | 2013-11-20 |
| PublicationDateYYYYMMDD | 2013-11-20 |
| PublicationDate_xml | – month: 11 year: 2013 text: 2013-11-20 day: 20 |
| PublicationDecade | 2010 |
| PublicationPlace | United States |
| PublicationPlace_xml | – name: United States – name: San Francisco – name: San Francisco, USA |
| PublicationTitle | PloS one |
| PublicationTitleAlternate | PLoS One |
| PublicationYear | 2013 |
| Publisher | Public Library of Science Public Library of Science (PLoS) |
| Publisher_xml | – name: Public Library of Science – name: Public Library of Science (PLoS) |
| References | ref12 GK Smyth (ref27) 2004; 3 B Gangadharan (ref28) 2007; 53 CF Staehler (ref11) 2012; 10 H Diao (ref16) 2012; 7 A Reverter (ref10) 2010; 26 LH Gan (ref33) 2011; 40 C Prieto (ref19) 2008; 3 ref18 MJ Mason (ref4) 2009; 10 W Huang da (ref35) 2009; 4 M Watson (ref13) 2006; 7 A Fukushima (ref14) 2013; 518 H Yu (ref5) 2011; 12 M Liu (ref17) 2013; 40 GE Lind (ref34) 2006; 28 MW Hao (ref30) 2002; 8 NJ Hudson (ref9) 2009; 5 ref20 L Gan (ref32) 2011; 6 KJ Archer (ref22) 2009; 18 M Kayano (ref7) 2011; 39 Q Liu (ref24) 2010; 11 LJ Wang (ref31) 2009; 379 A Reverter (ref1) 2006; 22 ref29 A Essaghir (ref23) 2010; 38 A van Nas (ref3) 2009; 150 LL Elo (ref21) 2007; 23 DJ Watts (ref26) 1998; 393 A de la Fuente (ref37) 2010; 26 JK Choi (ref2) 2005; 21 F Sohler (ref25) 2005; 21 Z Hu (ref36) 2006; 7 Y Choi (ref8) 2009; 25 BH Liu (ref6) 2010; 26 Z Qu (ref15) 2013; 68 |
| References_xml | – volume: 21 start-page: 4348 year: 2005 ident: ref2 article-title: Differential coexpression analysis using microarray data and its application to human cancer publication-title: Bioinformatics doi: 10.1093/bioinformatics/bti722 – volume: 38 start-page: e120 year: 2010 ident: ref23 article-title: Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data publication-title: Nucleic Acids Res doi: 10.1093/nar/gkq149 – volume: 393 start-page: 440 year: 1998 ident: ref26 article-title: Collective dynamics of ‘small-world’ networks publication-title: Nature doi: 10.1038/30918 – ident: ref18 doi: 10.1007/s10067-012-2143-9 – ident: ref20 – volume: 8 start-page: 203 year: 2002 ident: ref30 article-title: Transcription factor EGR-1 inhibits growth of hepatocellular carcinoma and esophageal carcinoma cell lines publication-title: World J Gastroenterol doi: 10.3748/wjg.v8.i2.203 – volume: 22 start-page: 2396 year: 2006 ident: ref1 article-title: Simultaneous identification of differential gene expression and connectivity in inflammation, adipogenesis and cancer publication-title: Bioinformatics doi: 10.1093/bioinformatics/btl392 – volume: 3 start-page: Article3 year: 2004 ident: ref27 article-title: Linear models and empirical bayes methods for assessing differential expression in microarray experiments publication-title: Stat Appl Genet Mol Biol doi: 10.2202/1544-6115.1027 – volume: 150 start-page: 1235 year: 2009 ident: ref3 article-title: Elucidating the role of gonadal hormones in sexually dimorphic gene coexpression networks publication-title: Endocrinology doi: 10.1210/en.2008-0563 – volume: 7 start-page: 509 year: 2006 ident: ref13 article-title: CoXpress: differential co-expression in gene expression data publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-7-509 – volume: 5 start-page: e1000382 year: 2009 ident: ref9 article-title: A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation publication-title: PLoS Comput Biol doi: 10.1371/journal.pcbi.1000382 – volume: 21 start-page: ii115 year: 2005 ident: ref25 article-title: Identifying active transcription factors and kinases from expression data using pathway queries publication-title: Bioinformatics doi: 10.1093/bioinformatics/bti1120 – volume: 7 start-page: 12 year: 2006 ident: ref36 article-title: Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-7-12 – volume: 26 start-page: 326 year: 2010 ident: ref37 article-title: From ‘differential expression’ to ‘differential networking’ - identification of dysfunctional regulatory networks in diseases publication-title: Trends Genet doi: 10.1016/j.tig.2010.05.001 – volume: 10 start-page: 285 year: 2012 ident: ref11 article-title: Whole miRNome-wide differential co-expression of microRNAs publication-title: Genomics Proteomics Bioinformatics doi: 10.1016/j.gpb.2012.08.003 – volume: 39 start-page: e74 year: 2011 ident: ref7 article-title: ROS-DET: robust detector of switching mechanisms in gene expression publication-title: Nucleic Acids Res doi: 10.1093/nar/gkr130 – volume: 3 start-page: e3911 year: 2008 ident: ref19 article-title: Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles publication-title: PLoS One doi: 10.1371/journal.pone.0003911 – volume: 53 start-page: 1792 year: 2007 ident: ref28 article-title: Novel serum biomarker candidates for liver fibrosis in hepatitis C patients publication-title: Clin Chem doi: 10.1373/clinchem.2007.089144 – volume: 40 start-page: 309 year: 2011 ident: ref33 article-title: DNA methylation of ZIC1 and KLOTHO gene promoters in colorectal carcinomas and its clinicopathological significance publication-title: Zhejiang Da Xue Xue Bao Yi Xue Ban – volume: 7 start-page: e52319 year: 2012 ident: ref16 article-title: Gene expression profiling combined with bioinformatics analysis identify biomarkers for Parkinson disease publication-title: PLoS One doi: 10.1371/journal.pone.0052319 – volume: 11 start-page: S5 year: 2010 ident: ref24 article-title: TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-11-S11-S5 – volume: 6 start-page: e16916 year: 2011 ident: ref32 article-title: ZIC1 is downregulated through promoter hypermethylation, and functions as a tumor suppressor gene in colorectal cancer publication-title: PLoS One doi: 10.1371/journal.pone.0016916 – volume: 68 start-page: 225 year: 2013 ident: ref15 article-title: Analysis of crucial molecules involved in herniated discs and degenerative disc disease publication-title: Clinics (Sao Paulo) doi: 10.6061/clinics/2013(02)OA17 – volume: 28 start-page: 259 year: 2006 ident: ref34 article-title: ADAMTS1, CRABP1, and NR3C1 identified as epigenetically deregulated genes in colorectal tumorigenesis publication-title: Cell Oncol – volume: 26 start-page: 896 year: 2010 ident: ref10 article-title: Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq051 – volume: 23 start-page: 2096 year: 2007 ident: ref21 article-title: Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process publication-title: Bioinformatics doi: 10.1093/bioinformatics/btm309 – volume: 12 start-page: 315 year: 2011 ident: ref5 article-title: Link-based quantitative methods to identify differentially coexpressed genes and gene pairs publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-12-315 – volume: 379 start-page: 959 year: 2009 ident: ref31 article-title: ZIC1 is downregulated through promoter hypermethylation in gastric cancer publication-title: Biochem Biophys Res Commun doi: 10.1016/j.bbrc.2008.12.180 – ident: ref12 doi: 10.1039/c2mb25434d – volume: 25 start-page: 2780 year: 2009 ident: ref8 article-title: Statistical methods for gene set co-expression analysis publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp502 – volume: 518 start-page: 209 year: 2013 ident: ref14 article-title: DiffCorr: an R package to analyze and visualize differential correlations in biological networks publication-title: Gene doi: 10.1016/j.gene.2012.11.028 – ident: ref29 doi: 10.1053/j.gastro.2009.08.005 – volume: 10 start-page: 327 year: 2009 ident: ref4 article-title: Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells publication-title: BMC Genomics doi: 10.1186/1471-2164-10-327 – volume: 26 start-page: 2637 year: 2010 ident: ref6 article-title: DCGL: an R package for identifying differentially coexpressed genes and links from gene expression microarray data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq471 – volume: 40 start-page: 3731 year: 2013 ident: ref17 article-title: Microarray gene expression profiling analysis combined with bioinformatics in multiple sclerosis publication-title: Mol Biol Rep doi: 10.1007/s11033-012-2449-3 – volume: 4 start-page: 44 year: 2009 ident: ref35 article-title: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources publication-title: Nat Protoc doi: 10.1038/nprot.2008.211 – volume: 18 start-page: 2929 year: 2009 ident: ref22 article-title: Identifying genes for establishing a multigenic test for hepatocellular carcinoma surveillance in hepatitis C virus-positive cirrhotic patients publication-title: Cancer Epidemiol Biomarkers Prev doi: 10.1158/1055-9965.EPI-09-0767 |
| SSID | ssj0053866 |
| Score | 2.4214401 |
| Snippet | Differential co-expression analysis (DCEA) has emerged in recent years as a novel, systematic investigation into gene expression data. While most DCEA studies... Motivation Differential co-expression analysis (DCEA) has emerged in recent years as a novel, systematic investigation into gene expression data. While most... Motivation To advance from DCEA to DRA, we upgraded the DCGL package from v1.0 to v2.0. A new module named "Differential Regulation Analysis" (DRA) was... Motivation Differential co-expression analysis (DCEA) has emerged in recent years as a novel, systematic investigation into gene expression data. While most... |
| SourceID | plos doaj pubmedcentral proquest gale pubmed crossref |
| SourceType | Open Website Open Access Repository Aggregation Database Index Database Enrichment Source |
| StartPage | e79729 |
| SubjectTerms | Algorithms Analysis Bioinformatics Biology Cell cycle Disease DNA methylation Gene expression Gene Regulatory Networks Genes Hepatitis HyperText Markup Language Informatics Java (programming language) Kinases Laboratories Links Liver cancer Medical research Medicine Oligonucleotide Array Sequence Analysis Regulations Researchers Servers Software Studies Transcription (Genetics) Transcription factors |
| SummonAdditionalLinks | – databaseName: DOAJ Directory of Open Access Journals dbid: DOA link: http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV3db9MwELdQxQMviI2PZXRgEBLwkC2xHdvhbQwGSNNAA6a9oMjxB1RUadW0FX8-59gNC5o0HnjtXar2dx8-K3e_Q-hZVlpFuHGpoiZLmWU6rXNWp5KXUlnlXNmtezs_Eaen8uKi_HRp1ZfvCQv0wAG4g5rUDqpsQXMtGHOQPQ1lLiOKZEwX3cg6yUS5uUyFHAxRzHkclKMiP4h22Z_PGuvJsstQUv45iDq-_j4rj-bTWXtVyfl35-Slo-j4Droda0h8GH77Frphm220FaO0xS8ilfTLu-jbm6N3J3hN9rNXWDX4DMMN-SdkEAylKl41azvx0-h4syUFon2KF2E7PdgL-9mToVDPUvsr9s4299DX47dfjt6ncaFCqnlJlinLFUQwlUyLwrmsNtwabgBNw4kmUomsMI6YvJam1sRJzQVlykDRwgphS0rvo1EDEO4gXDAuiTDCsFoxJ1yZkZpkAExRa-mITBDdoFvpyDbul15Mq-4VmoBbRwCr8japok0SlPZPzQPbxjX6r73hel3Pld19AB5URQ-qrvOgBD32Zq_C4Gkf8dWhn8KVnFKRoKedhufLaHxDzne1atvqw8fzf1D6fDZQeh6V3Azg0CoOQcB_8jxcA83xQBOiXg_EO95JN6i0_goXyAIBlPHGca8WP-nF_kt9k11jZ6tOx28ogxI5QQ-Cn_fIEr-SJedFgsQgAgbQDyXN5EdHV06hyJcF2_0ftnqIbhG_jyTPIb2P0Wi5WNk9dFOvl5N28ajLAb8BkJZgbA priority: 102 providerName: Directory of Open Access Journals – databaseName: Public Library of Science (PLoS) Journals Open Access dbid: FPL link: http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1bb9MwFLagXMQLsHJZoIBBSMBDRmI7tsNb6SgglVEVNu0FRY4vUFEl1dJW8O-xEzeQaRPw2nNSJZ99jo9ln-8D4GmUaoGoMqHAKgqJJjLMY5KHnKZcaGFMWsu9HU3YwQE_Pk6nvzeKp07wMYtfekz3lmWhHdF1asvBi-ASwpQ6qYbxdLLNvDZ2KfXtcec92Vl-apb-Nhf3louyOqvQPH1f8o8FaHzjf1_9JrjuS004bObGDrigiz640ohP_uyDqx_8sXof7PgIr-BzT0P94hb4sj96O4EbtBe9gsMCzuBUyO82-0Bb5sLDYqPnrpMd7nuFFZspFnDWKNvbsYaub6VrHJWh_uHv3Ra3weH4zefRu9CLMYSSpmgVkljY6MecSJYYE-WKakUVMZGiSCIuWJQog1Scc5VLZLikDBOhbMFDEqZTjO-AXmFx2AUwIZQjppgiuSCGmTRCOYosvEkuuUE8AHg7Rpn0TOVOMGOR1cdvzO5YGgQzB2zmgQ1A2D61bJg6_uL_2g1_6-t4tusf7AhmPmyzHOXG7vEYjiUjxNi1W2H7zUigiMiExAF45CZP1jStttkiG7oOXk4xZgF4Uns4ro3CXeb5KtZVlb3_ePQPTp9mHadn3smUFg4pfAOF_SbH4dXxHHQ8bcaQHfOum-pbVCq3_WuIBi0og-30P9v8uDW7P3UX9Apdrmsfp25my-sA3G2ipUUWOTmXmCYBYJ046kDftRTzbzXVObYbBJ6Qe-e_8X1wDTmFkji2CX8AequTtX4ALsvNal6dPKzzwy9SXGM0 priority: 102 providerName: Public Library of Science |
| Title | DCGL v2.0: An R Package for Unveiling Differential Regulation from Differential Co-expression |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/24278165 https://www.proquest.com/docview/1460160719 https://www.proquest.com/docview/1462186264 https://pubmed.ncbi.nlm.nih.gov/PMC3835854 https://doaj.org/article/b2bf960731c744f299d34f02a204c541 http://dx.doi.org/10.1371/journal.pone.0079729 |
| Volume | 8 |
| WOSCitedRecordID | wos000327313100041&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| journalDatabaseRights | – providerCode: PRVAON databaseName: Directory of Open Access Journals customDbUrl: eissn: 1932-6203 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0053866 issn: 1932-6203 databaseCode: DOA dateStart: 20060101 isFulltext: true titleUrlDefault: https://www.doaj.org/ providerName: Directory of Open Access Journals – providerCode: PRVHPJ databaseName: ROAD: Directory of Open Access Scholarly Resources customDbUrl: eissn: 1932-6203 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0053866 issn: 1932-6203 databaseCode: M~E dateStart: 20060101 isFulltext: true titleUrlDefault: https://road.issn.org providerName: ISSN International Centre – providerCode: PRVPQU databaseName: Advanced Technologies & Aerospace Database customDbUrl: eissn: 1932-6203 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0053866 issn: 1932-6203 databaseCode: P5Z dateStart: 20061201 isFulltext: true titleUrlDefault: https://search.proquest.com/hightechjournals providerName: ProQuest – providerCode: PRVPQU databaseName: Agricultural Science Database customDbUrl: eissn: 1932-6203 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0053866 issn: 1932-6203 databaseCode: M0K dateStart: 20061201 isFulltext: true titleUrlDefault: https://search.proquest.com/agriculturejournals providerName: ProQuest – providerCode: PRVPQU databaseName: Biological Science Database customDbUrl: eissn: 1932-6203 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0053866 issn: 1932-6203 databaseCode: M7P dateStart: 20061201 isFulltext: true titleUrlDefault: http://search.proquest.com/biologicalscijournals providerName: ProQuest – providerCode: PRVPQU databaseName: Engineering Database customDbUrl: eissn: 1932-6203 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0053866 issn: 1932-6203 databaseCode: M7S dateStart: 20061201 isFulltext: true titleUrlDefault: http://search.proquest.com providerName: ProQuest – providerCode: PRVPQU databaseName: Environmental Science Database customDbUrl: eissn: 1932-6203 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0053866 issn: 1932-6203 databaseCode: PATMY dateStart: 20061201 isFulltext: true titleUrlDefault: http://search.proquest.com/environmentalscience providerName: ProQuest – providerCode: PRVPQU databaseName: Health & Medical Collection (ProQuest) customDbUrl: eissn: 1932-6203 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0053866 issn: 1932-6203 databaseCode: 7X7 dateStart: 20061201 isFulltext: true titleUrlDefault: https://search.proquest.com/healthcomplete providerName: ProQuest – providerCode: PRVPQU databaseName: Materials Science Database customDbUrl: eissn: 1932-6203 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0053866 issn: 1932-6203 databaseCode: KB. dateStart: 20061201 isFulltext: true titleUrlDefault: http://search.proquest.com/materialsscijournals providerName: ProQuest – providerCode: PRVPQU databaseName: Nursing & Allied Health Database customDbUrl: eissn: 1932-6203 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0053866 issn: 1932-6203 databaseCode: 7RV dateStart: 20061201 isFulltext: true titleUrlDefault: https://search.proquest.com/nahs providerName: ProQuest – providerCode: PRVPQU databaseName: ProQuest Central customDbUrl: eissn: 1932-6203 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0053866 issn: 1932-6203 databaseCode: BENPR dateStart: 20061201 isFulltext: true titleUrlDefault: https://www.proquest.com/central providerName: ProQuest – providerCode: PRVPQU databaseName: Public Health Database customDbUrl: eissn: 1932-6203 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0053866 issn: 1932-6203 databaseCode: 8C1 dateStart: 20061201 isFulltext: true titleUrlDefault: https://search.proquest.com/publichealth providerName: ProQuest – providerCode: PRVPQU databaseName: Publicly Available Content Database customDbUrl: eissn: 1932-6203 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0053866 issn: 1932-6203 databaseCode: PIMPY dateStart: 20061201 isFulltext: true titleUrlDefault: http://search.proquest.com/publiccontent providerName: ProQuest – providerCode: PRVATS databaseName: Public Library of Science (PLoS) Journals Open Access customDbUrl: eissn: 1932-6203 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0053866 issn: 1932-6203 databaseCode: FPL dateStart: 20060101 isFulltext: true titleUrlDefault: http://www.plos.org/publications/ providerName: Public Library of Science |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV3db9MwELdYB4gXYOVjhVECQmI8pEscJ3Z4QW23wbS2RB2rChKKEjseE1NSlq6C_56z43YETYDEyz3E56o-n38-2_eB0AsnzBIcCGknnnBskhFupy5JbRaELMkSKUNd7m0yoKMRm07DyFy4lcatcomJGqhFwdUd-Q6s6CoZWvhm9s1WVaPU66opobGG1lWWBKxd96IlEsNaDgITLudRd8fMTmdW5JlKmR1WhuXldqSz9q-wuTE7K8qrDM_f_Sd_2ZD27_zvUO6i28YUtbqV7myga1neRDeq4pQ_mujm0Dy7N9GGQYDS2jZpql_dQ593-28H1gJ3nNdWN7fGVpTwr4BOFpjB1nG-yE5VpLu1ayqwAJKcWeOq8j3ogqXiWuqN_cLOvhu_3Pw-Ot7f-9B_Z5tiDTYPQjy3iZsAOniMcOpL6aQiyEQgiHREgDlmCXV8IbFwUyZSjiXjAfVIIsAgIj7NQs97gBo5TMwmsnwSMEwFFSRNiKQydHCKHRC3n3ImMWshbzlnMTeZzFVBjbNYP89RONFUEozVTMdmplvIXvWaVZk8_sLfU-qw4lV5uPWH4vwkNss6TnEq4QxIPZdTQiTs7cKDMeMEO4T7xG2hp0qZ4iqodYUmcVdF-LLA82gLPdccKhdHrpx9TpKLsowP3k_-geloXGN6aZhkAeLgiQmwgDGpHF81zq0aJyAKrzVvKtVfSqWMLxUWei5V-urmZ6tm9aPKgS_PigvNo6qfgfndQg-r1bOSLFblXtzAbyFaW1c10ddb8tMvOhW6BwcI5pNHf_5bj9EtrKqYuC5sCluoMT-_yJ6g63wxPy3P22iNjieKTqmmDCjru2203tsbReO2vqYBuh8NgB72OkCHzmFbY42mR0Aj_xP0iA6G0cefMIOBZg |
| linkProvider | ProQuest |
| linkToHtml | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw1V1Lb9NAEF5V4XkBGh41FLogEHBwa6_XXhsJoZBQGuXRKrRVL8jY-wgRkR3iJNA_xW9k1167GFXApQeumbGVHc98u2PPzAfAUyvgEfKYMCOHWSbmmJqxjWPT9wI_4pEQQU73dtwnw6F_chIcrIEfZS-MKqssMTEHapZS9Y58R0Z0MQwteDP7airWKPV1taTQKNyix0-_yZQte93tyOf7DKHdd4ftPVOzCpjUC9DCxHYk3djxMSWuEFbMPM48hoXFPESRHxHLZQIxO_ZZTJHwqUccHDG5c2OX8EC9AJWQfwnLxEuVkA2sXon8Ejs8T7fnOcTe0d6wPUsTrkZ0B8VB9mz7y1kCqr2gMZum2XkH3d_rNX_ZAHdv_m-muwVu6KM2bBWxsQ7WeNIEVwryzdMmuDrQZQVNsK4RLoMv9Bjul7fBx077fR-u0Lb1CrYSOIIHEf0i0RfKYz48SlZ8ojr5YUczzEiknMIRH2s6NKj6durCdmry77ruOLkDji5k7XdBI5GOsAGgiz0fEUYYjiMsiAgsFCNLPl43pr5AvgGc0kdCqie1K8KQaZh_fiQyYyssGCrPCrVnGcCsrpoVk0r-ov9WuV-lq-aM5z-k83GoYSuMUSxkjkscmxKMhTy7MEeuGUXIwtTFtgG2lPOGRdNuhZZhS3Uw-57jEAM8yTXUrJFEFTONo2WWhd39439Q-jCqKT3XSiKV5qCRbiCRa1IzzGqamzVNiZi0Jt5QoVZaJQvPAkReWYbQ-eLHlVjdVBUoJjxd5jqK3U2mFwa4V0RrZVmk6GxszzUAqcVxzfR1STL5nI96d2SC5Lv4_p__1ha4tnc46If97rD3AFxHirHFtuUGuAkai_mSPwSX6WoxyeaPcryC4NNFR_lP51DR_A |
| linkToPdf | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw1V1Lb9NAEF5VASouQMujgUIXBAIObu312msjIRQaClFDiAqtekHG3keIiOwQJ4H-NX4ds_baxagCLj1wzYwj73jmm117Zj6EHtqhjIkvlBW7wraopNxKHJpYgR8GsYyVCgu6t6M-GwyC4-NwuIJ-VL0wuqyywsQCqEXG9TvyHYjochhauKNMWcSwu_di-tXSDFL6S2tFp1G6yL48-QbHt_x5rwvP-hEhe68-7L6xDMOAxf2QzC3qxODSbkA585SyE-FL4QuqbOETToKY2Z5QRDhJIBJOVMB95tJYQBanHpOhfhkK8H-Bwb2RomxwWGUBwBHfN616LnN2jGdsT7NU6nHdYbmpPU2FBWNAnRda00mWn7Xp_b1285dkuHf1fzbjNXTFbMFxp4yZNbQi03V0qSTlPFlHq29NucE6WjPIl-MnZjz30-voY3f3dR8vybb9DHdSfICHMf8CqIxh-48P06Uc6w5_3DXMM4CgE3wgR4YmDet-nqZwN7Pkd1OPnN5Ah-ey9puolYJTbCDsUT8gTDBBk5gqpkKbJMSGR-0lPFAkaCO38peImwnumkhkEhWfJRmc5EoLRtrLIuNlbWTVV03LCSZ_0X-pXbHW1fPHix-y2SgycBYlJFFw9mWuwxmlCvY0woU1k5jYlHvUaaMt7chR2cxbo2jU0Z3Nge-6rI0eFBp6Bkmq3XAUL_I86r07-gel9wcNpcdGSWVgDh6bxhJYk55t1tDcbGgCkvKGeEOHXWWVPDoNFriyCqezxfdrsf5TXbiYymxR6GjWNzh2tNGtMnJryxJNc-P4XhuxRkw3TN-UpOPPxQh4Fw5OgUdv__m2ttAqBHfU7w3276DLRBO5OA7kxU3Ums8W8i66yJfzcT67V0AXRp_OO8h_Aky92tM |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=DCGL+v2.0%3A+an+R+package+for+unveiling+differential+regulation+from+differential+co-expression&rft.jtitle=PloS+one&rft.au=Yang%2C+Jing&rft.au=Yu%2C+Hui&rft.au=Liu%2C+Bao-Hong&rft.au=Zhao%2C+Zhongming&rft.date=2013-11-20&rft.issn=1932-6203&rft.eissn=1932-6203&rft.volume=8&rft.issue=11&rft.spage=e79729&rft_id=info:doi/10.1371%2Fjournal.pone.0079729&rft.externalDBID=NO_FULL_TEXT |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1932-6203&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1932-6203&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1932-6203&client=summon |