Volcano plots in analyzing differential expressions with mRNA microarrays
A volcano plot displays unstandardized signal (e.g. log-fold-change) against noise-adjusted/standardized signal (e.g. t-statistic or -log(10)(p-value) from the t-test). We review the basic and interactive use of the volcano plot and its crucial role in understanding the regularized t-statistic. The...
Gespeichert in:
| Veröffentlicht in: | Journal of bioinformatics and computational biology Jg. 10; H. 6; S. 1231003 |
|---|---|
| 1. Verfasser: | |
| Format: | Journal Article |
| Sprache: | Englisch |
| Veröffentlicht: |
Singapore
01.12.2012
|
| Schlagworte: | |
| ISSN: | 1757-6334, 1757-6334 |
| Online-Zugang: | Weitere Angaben |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| Abstract | A volcano plot displays unstandardized signal (e.g. log-fold-change) against noise-adjusted/standardized signal (e.g. t-statistic or -log(10)(p-value) from the t-test). We review the basic and interactive use of the volcano plot and its crucial role in understanding the regularized t-statistic. The joint filtering gene selection criterion based on regularized statistics has a curved discriminant line in the volcano plot, as compared to the two perpendicular lines for the "double filtering" criterion. This review attempts to provide a unifying framework for discussions on alternative measures of differential expression, improved methods for estimating variance, and visual display of a microarray analysis result. We also discuss the possibility of applying volcano plots to other fields beyond microarray. |
|---|---|
| AbstractList | A volcano plot displays unstandardized signal (e.g. log-fold-change) against noise-adjusted/standardized signal (e.g. t-statistic or -log(10)(p-value) from the t-test). We review the basic and interactive use of the volcano plot and its crucial role in understanding the regularized t-statistic. The joint filtering gene selection criterion based on regularized statistics has a curved discriminant line in the volcano plot, as compared to the two perpendicular lines for the "double filtering" criterion. This review attempts to provide a unifying framework for discussions on alternative measures of differential expression, improved methods for estimating variance, and visual display of a microarray analysis result. We also discuss the possibility of applying volcano plots to other fields beyond microarray. A volcano plot displays unstandardized signal (e.g. log-fold-change) against noise-adjusted/standardized signal (e.g. t-statistic or -log(10)(p-value) from the t-test). We review the basic and interactive use of the volcano plot and its crucial role in understanding the regularized t-statistic. The joint filtering gene selection criterion based on regularized statistics has a curved discriminant line in the volcano plot, as compared to the two perpendicular lines for the "double filtering" criterion. This review attempts to provide a unifying framework for discussions on alternative measures of differential expression, improved methods for estimating variance, and visual display of a microarray analysis result. We also discuss the possibility of applying volcano plots to other fields beyond microarray.A volcano plot displays unstandardized signal (e.g. log-fold-change) against noise-adjusted/standardized signal (e.g. t-statistic or -log(10)(p-value) from the t-test). We review the basic and interactive use of the volcano plot and its crucial role in understanding the regularized t-statistic. The joint filtering gene selection criterion based on regularized statistics has a curved discriminant line in the volcano plot, as compared to the two perpendicular lines for the "double filtering" criterion. This review attempts to provide a unifying framework for discussions on alternative measures of differential expression, improved methods for estimating variance, and visual display of a microarray analysis result. We also discuss the possibility of applying volcano plots to other fields beyond microarray. |
| Author | Li, Wentian |
| Author_xml | – sequence: 1 givenname: Wentian surname: Li fullname: Li, Wentian email: wtli2012@gmail.com organization: The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, 350 Community Drive, NY 11030, USA. wtli2012@gmail.com |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/23075208$$D View this record in MEDLINE/PubMed |
| BookMark | eNpNj8tKAzEARYNUtFY_wI1k6WY076TLUnwUioKv7ZBMEg1kkjGZovXrFazg6tzF4cI5ApOUkwPgFKMLjBm5fEQEzyVBCBOKEaJqD0yx5LIRlLLJv30ADglFkhOkpmD1kmOnU4ZDzGOFIUGddNx-hfQKbfDeFZfGoCN0n0NxtYacKvwI4xvsH-4WsA9dyboUva3HYN_rWN3JjjPwfH31tLxt1vc3q-Vi3XRUctUQwyTqvLBUceG4IQIJbxmRQlDEiUfOd8wwI-bUSuMs41ogohQxXlvvNJmB89_foeT3jatj24fauRh1cnlTW4wxnSuMmPxRz3bqxvTOtkMJvS7b9i-ffANuBVvx |
| CitedBy_id | crossref_primary_10_1016_j_jcf_2019_02_009 crossref_primary_10_3390_ijms26178218 crossref_primary_10_1186_s12864_019_6358_x crossref_primary_10_3390_genes15101244 crossref_primary_10_1002_pmic_201400377 crossref_primary_10_1016_j_jprot_2014_06_029 crossref_primary_10_4137_BBI_S12494 crossref_primary_10_1111_raq_12146 crossref_primary_10_1159_000500688 crossref_primary_10_1186_s13040_019_0202_3 crossref_primary_10_1016_j_scitotenv_2023_165324 crossref_primary_10_1007_s00438_017_1316_2 crossref_primary_10_3389_fimmu_2019_00516 crossref_primary_10_1007_s12561_024_09446_5 crossref_primary_10_1038_s41598_023_43593_x crossref_primary_10_3390_cancers12030669 crossref_primary_10_1016_j_fuel_2021_120317 crossref_primary_10_1016_j_taap_2020_114898 crossref_primary_10_1371_journal_pcbi_1007912 crossref_primary_10_1111_jcmm_16976 crossref_primary_10_1016_j_envint_2024_108923 crossref_primary_10_1038_nsmb_3076 crossref_primary_10_1371_journal_pone_0300461 crossref_primary_10_1016_j_fuel_2023_129915 crossref_primary_10_1038_s41598_021_86809_8 crossref_primary_10_1371_journal_pgen_1009600 crossref_primary_10_3389_fvets_2021_625609 crossref_primary_10_3390_biomedicines12081639 crossref_primary_10_3389_fgene_2020_573877 crossref_primary_10_1016_j_compbiolchem_2013_02_003 crossref_primary_10_1007_s00604_018_3090_1 crossref_primary_10_1073_pnas_2005634117 crossref_primary_10_1186_s12929_017_0383_3 crossref_primary_10_1186_s40001_023_01193_5 crossref_primary_10_2147_JIR_S360498 crossref_primary_10_1038_s41385_022_00553_4 crossref_primary_10_1080_15287394_2017_1408201 crossref_primary_10_1371_journal_pone_0283702 crossref_primary_10_3390_ani13060958 crossref_primary_10_1016_j_compbiolchem_2017_10_010 crossref_primary_10_3390_brainsci9010001 crossref_primary_10_1038_s41598_020_59978_1 crossref_primary_10_1161_CIRCGENETICS_114_000505 crossref_primary_10_1093_jxb_erv120 crossref_primary_10_1186_s12864_020_6550_z crossref_primary_10_1016_j_jbi_2016_10_012 crossref_primary_10_1186_s13023_019_1008_6 crossref_primary_10_1007_s12640_015_9529_9 crossref_primary_10_1371_journal_pone_0142801 crossref_primary_10_1016_j_conctc_2023_101101 crossref_primary_10_1088_1752_7163_ab9f8a crossref_primary_10_1371_journal_pgen_1007494 crossref_primary_10_1016_j_exer_2018_05_026 crossref_primary_10_1097_CM9_0000000000001773 crossref_primary_10_1186_s12859_018_2117_2 crossref_primary_10_1002_pd_5893 crossref_primary_10_1186_s13040_024_00369_x crossref_primary_10_1016_j_comtox_2020_100138 crossref_primary_10_1080_08982112_2017_1381487 crossref_primary_10_1182_blood_2013_08_520031 crossref_primary_10_1016_j_aca_2019_11_006 crossref_primary_10_1111_imm_12894 crossref_primary_10_1534_g3_119_400291 crossref_primary_10_1080_14789450_2016_1181546 crossref_primary_10_3390_medicina55060269 crossref_primary_10_1016_j_foodchem_2019_03_101 crossref_primary_10_1016_j_ijhydene_2020_03_108 crossref_primary_10_1007_s10522_024_10104_y crossref_primary_10_1371_journal_pone_0304632 crossref_primary_10_3390_cancers11071003 crossref_primary_10_3389_fimmu_2016_00272 crossref_primary_10_1080_10618600_2019_1598871 crossref_primary_10_3892_mmr_2020_11477 crossref_primary_10_3389_fimmu_2018_02870 crossref_primary_10_1186_s12859_023_05360_7 crossref_primary_10_1177_11772719221088404 crossref_primary_10_1214_19_AOS1847 crossref_primary_10_3390_ijms241914581 crossref_primary_10_7717_peerj_1360 crossref_primary_10_1210_jc_2018_00352 crossref_primary_10_1038_s41598_020_76603_3 crossref_primary_10_1002_ece3_8920 crossref_primary_10_1186_s12951_025_03560_2 crossref_primary_10_3390_cells8010072 crossref_primary_10_3390_ijms22115959 crossref_primary_10_1186_s12864_021_07756_2 crossref_primary_10_1038_s41598_023_28234_7 crossref_primary_10_1186_1868_7083_6_12 crossref_primary_10_1080_01621459_2021_1920958 crossref_primary_10_1080_07853890_2022_2048064 crossref_primary_10_1016_j_gene_2018_01_008 crossref_primary_10_3389_fmicb_2020_577497 crossref_primary_10_1007_s00417_018_3905_0 crossref_primary_10_1016_j_chmed_2022_06_009 crossref_primary_10_1186_s13046_019_1458_7 crossref_primary_10_1016_j_chemosphere_2023_139682 crossref_primary_10_1038_srep29477 crossref_primary_10_3390_membranes12020154 crossref_primary_10_1002_mnfr_201900558 crossref_primary_10_1016_j_humgen_2025_201378 crossref_primary_10_1038_s41598_017_14674_5 crossref_primary_10_1038_s41598_025_18172_x crossref_primary_10_1007_s10681_019_2351_3 crossref_primary_10_1186_s12859_023_05167_6 crossref_primary_10_1111_jne_12628 crossref_primary_10_7717_peerj_12091 crossref_primary_10_1002_cam4_540 crossref_primary_10_1007_s11356_017_8977_6 crossref_primary_10_1155_2020_2613091 crossref_primary_10_1109_MDAT_2023_3317337 crossref_primary_10_1111_mmi_14717 crossref_primary_10_1002_jcp_28920 crossref_primary_10_1038_s41598_020_72068_6 crossref_primary_10_1371_journal_pone_0091840 |
| ContentType | Journal Article |
| DBID | CGR CUY CVF ECM EIF NPM 7X8 |
| DOI | 10.1142/S0219720012310038 |
| DatabaseName | Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed MEDLINE - Academic |
| DatabaseTitle | MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) MEDLINE - Academic |
| DatabaseTitleList | MEDLINE MEDLINE - Academic |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: 7X8 name: MEDLINE - Academic url: https://search.proquest.com/medline sourceTypes: Aggregation Database |
| DeliveryMethod | no_fulltext_linktorsrc |
| EISSN | 1757-6334 |
| ExternalDocumentID | 23075208 |
| Genre | Journal Article Review |
| GroupedDBID | CGR CUY CVF ECM EIF NPM 7X8 |
| ID | FETCH-LOGICAL-c3758-2b470cf6d3856e5b2606fd427663052f0efc4b4b693d7bed45a602882bfadfea2 |
| IEDL.DBID | 7X8 |
| ISICitedReferencesCount | 146 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000310084500002&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| ISSN | 1757-6334 |
| IngestDate | Thu Jul 10 21:01:26 EDT 2025 Thu Jan 02 23:10:38 EST 2025 |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 6 |
| Language | English |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c3758-2b470cf6d3856e5b2606fd427663052f0efc4b4b693d7bed45a602882bfadfea2 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 ObjectType-Review-3 content type line 23 |
| PMID | 23075208 |
| PQID | 1113981047 |
| PQPubID | 23479 |
| ParticipantIDs | proquest_miscellaneous_1113981047 pubmed_primary_23075208 |
| PublicationCentury | 2000 |
| PublicationDate | 2012-Dec 20121201 |
| PublicationDateYYYYMMDD | 2012-12-01 |
| PublicationDate_xml | – month: 12 year: 2012 text: 2012-Dec |
| PublicationDecade | 2010 |
| PublicationPlace | Singapore |
| PublicationPlace_xml | – name: Singapore |
| PublicationTitle | Journal of bioinformatics and computational biology |
| PublicationTitleAlternate | J Bioinform Comput Biol |
| PublicationYear | 2012 |
| Score | 2.376974 |
| SecondaryResourceType | review_article |
| Snippet | A volcano plot displays unstandardized signal (e.g. log-fold-change) against noise-adjusted/standardized signal (e.g. t-statistic or -log(10)(p-value) from the... |
| SourceID | proquest pubmed |
| SourceType | Aggregation Database Index Database |
| StartPage | 1231003 |
| SubjectTerms | Animals Gene Expression Profiling - methods Humans Models, Statistical Oligonucleotide Array Sequence Analysis - methods Oligonucleotide Array Sequence Analysis - statistics & numerical data RNA, Messenger - genetics RNA, Messenger - metabolism Software |
| Title | Volcano plots in analyzing differential expressions with mRNA microarrays |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/23075208 https://www.proquest.com/docview/1113981047 |
| Volume | 10 |
| WOSCitedRecordID | wos000310084500002&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| hasFullText | |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV1LS8QwEA7qevDiA1_riwhey6ZpmrQnWcRFQcvii72VPGFht123q6i_3knbxZMgeMmlBMpkJvPNzJcZhC7AYojUBqKThLCAaUcDQBkiEKkTzGgS6-ak70SWJaNROmwTblVLq1zeifVFbUrtc-Q9PxI9TXxjgcvZa-CnRvnqajtCYxV1IvjstVqM6tdvIhYBjyLWFjJDRnuP4M5SQWsUEfqK2O-gsnYug63__tY22mxhJe43erCDVmyxi25fyglIrsSzSbmo8LjA0rcg-QJvhZeDUcDAJ9h-tHTYosI-MYunD1kfTz1XT87n8rPaQ8-D66erm6AdnRDoCCKAgComiHbcREnMbawgauHOMCoAYJCYOmKdZoopnkZGKGtYLDkgjYQqJ42zku6jtaIs7CHCythQhTxWkYFoSkvFQy4ZSVIaGmJD3UXnS8nkoJq-3iALW75V-Y9suuigEW8-a3po5J5_HlOSHP1h9zHaAJhCGxLJCeo4MEx7itb1-2Jczc_qM4c1G95_A2qkt-I |
| linkProvider | ProQuest |
| 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=Volcano+plots+in+analyzing+differential+expressions+with+mRNA+microarrays&rft.jtitle=Journal+of+bioinformatics+and+computational+biology&rft.au=Li%2C+Wentian&rft.date=2012-12-01&rft.issn=1757-6334&rft.eissn=1757-6334&rft.volume=10&rft.issue=6&rft.spage=1231003&rft_id=info:doi/10.1142%2FS0219720012310038&rft.externalDBID=NO_FULL_TEXT |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1757-6334&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1757-6334&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1757-6334&client=summon |