Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation
Gene-expression profiling has become a mainstay in immunology, but subtle changes in gene networks related to biological processes are hard to discern when comparing various datasets. For instance, conservation of the transcriptional response to sepsis in mouse models and human disease remains contr...
Uloženo v:
| Vydáno v: | Immunity (Cambridge, Mass.) Ročník 44; číslo 1; s. 194 - 206 |
|---|---|
| Hlavní autoři: | , , , , , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
| Vydáno: |
United States
19.01.2016
|
| Témata: | |
| ISSN: | 1097-4180 |
| On-line přístup: | Zjistit podrobnosti o přístupu |
| Tagy: |
Přidat tag
Žádné tagy, Buďte první, kdo vytvoří štítek k tomuto záznamu!
|
| Abstract | Gene-expression profiling has become a mainstay in immunology, but subtle changes in gene networks related to biological processes are hard to discern when comparing various datasets. For instance, conservation of the transcriptional response to sepsis in mouse models and human disease remains controversial. To improve transcriptional analysis in immunology, we created ImmuneSigDB: a manually annotated compendium of ∼5,000 gene-sets from diverse cell states, experimental manipulations, and genetic perturbations in immunology. Analysis using ImmuneSigDB identified signatures induced in activated myeloid cells and differentiating lymphocytes that were highly conserved between humans and mice. Sepsis triggered conserved patterns of gene expression in humans and mouse models. However, we also identified species-specific biological processes in the sepsis transcriptional response: although both species upregulated phagocytosis-related genes, a mitosis signature was specific to humans. ImmuneSigDB enables granular analysis of transcriptomic data to improve biological understanding of immune processes of the human and mouse immune systems. |
|---|---|
| AbstractList | Gene-expression profiling has become a mainstay in immunology, but subtle changes in gene networks related to biological processes are hard to discern when comparing various datasets. For instance, conservation of the transcriptional response to sepsis in mouse models and human disease remains controversial. To improve transcriptional analysis in immunology, we created ImmuneSigDB: a manually annotated compendium of ∼5,000 gene-sets from diverse cell states, experimental manipulations, and genetic perturbations in immunology. Analysis using ImmuneSigDB identified signatures induced in activated myeloid cells and differentiating lymphocytes that were highly conserved between humans and mice. Sepsis triggered conserved patterns of gene expression in humans and mouse models. However, we also identified species-specific biological processes in the sepsis transcriptional response: although both species upregulated phagocytosis-related genes, a mitosis signature was specific to humans. ImmuneSigDB enables granular analysis of transcriptomic data to improve biological understanding of immune processes of the human and mouse immune systems. |
| Author | Godec, Jernej Tan, Yan Mesirov, Jill P Bhattacharya, Sanchita Butte, Atul J Tamayo, Pablo Haining, W Nicholas Liberzon, Arthur |
| Author_xml | – sequence: 1 givenname: Jernej surname: Godec fullname: Godec, Jernej organization: Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA – sequence: 2 givenname: Yan surname: Tan fullname: Tan, Yan organization: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Bioinformatics Program, Boston University, Boston, MA 02215, USA – sequence: 3 givenname: Arthur surname: Liberzon fullname: Liberzon, Arthur organization: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA – sequence: 4 givenname: Pablo surname: Tamayo fullname: Tamayo, Pablo organization: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA – sequence: 5 givenname: Sanchita surname: Bhattacharya fullname: Bhattacharya, Sanchita organization: Institute for Computational Health Science, University of California, San Francisco, San Francisco, CA 94158, USA – sequence: 6 givenname: Atul J surname: Butte fullname: Butte, Atul J organization: Institute for Computational Health Science, University of California, San Francisco, San Francisco, CA 94158, USA – sequence: 7 givenname: Jill P surname: Mesirov fullname: Mesirov, Jill P organization: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Bioinformatics Program, Boston University, Boston, MA 02215, USA – sequence: 8 givenname: W Nicholas surname: Haining fullname: Haining, W Nicholas email: nicholas_haining@dfci.harvard.edu organization: Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Hematology/Oncology, Children's Hospital, Harvard Medical School, Boston, MA 02115, USA. Electronic address: nicholas_haining@dfci.harvard.edu |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/26795250$$D View this record in MEDLINE/PubMed |
| BookMark | eNo1kEtLxDAUhYMozkP_gUiWblqTtGmbpRYfhQHB0XVJm5shQ5PUphXm39vRES6cw-HjW9wVOnfeAUI3lMSU0Ox-HxtrJ2diRiiPKYsJyc7QkhKRRyktyAKtQtgTQlMuyCVasCwXnHGyRLb0tgenzGSx17g6agBvzc7JcRog4EqBG402cy29CzB8g8LSKbztoZ3X6De1afGj8Z3fHbBx-B1Cf4Tx6HHldCetlaPx7gpdaNkFuD7lGn0-P32Ur9Hm7aUqHzZRy0U6RlnSSNEkWrdMFgUv2iwVSkIm5qNENg3VLagkF0xrSlSjFAPJaJpDzosUOFujuz9vP_ivCcJYWxNa6DrpwE-hpnlGilklihm9PaFTY0HV_WCsHA71_4vYD1J3bJI |
| CitedBy_id | crossref_primary_10_1016_j_it_2021_10_007 crossref_primary_10_1016_j_crmeth_2022_100167 crossref_primary_10_1016_j_crmeth_2023_100563 crossref_primary_10_1073_pnas_2023050118 crossref_primary_10_1096_fj_202402318R crossref_primary_10_3389_fimmu_2019_03065 crossref_primary_10_1093_bib_bbae368 crossref_primary_10_1038_s41467_020_15298_6 crossref_primary_10_1128_IAI_00364_17 crossref_primary_10_1016_j_isci_2024_110096 crossref_primary_10_1080_2162402X_2021_1992880 crossref_primary_10_1093_bib_bbac064 crossref_primary_10_1164_rccm_201601_0107OC crossref_primary_10_1016_j_heliyon_2024_e32783 crossref_primary_10_3389_fimmu_2021_750665 crossref_primary_10_1097_MD_0000000000033990 crossref_primary_10_1186_s12859_020_3366_4 crossref_primary_10_1016_j_xpro_2024_103066 crossref_primary_10_1186_s12864_018_5217_5 crossref_primary_10_1186_s13046_021_02092_5 crossref_primary_10_1136_jitc_2025_011807 crossref_primary_10_1038_ni_3795 crossref_primary_10_1534_genetics_116_189498 crossref_primary_10_1016_j_stem_2018_12_011 crossref_primary_10_1186_s12920_018_0340_3 crossref_primary_10_3389_fimmu_2022_1092370 crossref_primary_10_3390_ijms25105491 crossref_primary_10_1038_s41467_019_13855_2 crossref_primary_10_1002_eji_201747174 crossref_primary_10_3389_fonc_2022_1031174 crossref_primary_10_1016_j_scitotenv_2022_160163 crossref_primary_10_1186_s12859_023_05397_8 crossref_primary_10_3389_fonc_2022_967207 crossref_primary_10_1038_s41467_022_31941_w crossref_primary_10_1136_jitc_2023_007288 crossref_primary_10_1371_journal_pone_0256442 crossref_primary_10_1038_s41590_022_01210_5 crossref_primary_10_1038_s41598_019_57207_y crossref_primary_10_1158_2159_8290_CD_17_0222 crossref_primary_10_2147_JIR_S307305 crossref_primary_10_3389_fimmu_2024_1470368 crossref_primary_10_3389_fgene_2023_1121018 crossref_primary_10_3389_fonc_2021_685026 crossref_primary_10_1172_JCI137712 crossref_primary_10_1016_j_chom_2021_03_015 crossref_primary_10_1089_cmb_2023_0278 crossref_primary_10_1016_j_aquatox_2025_107484 crossref_primary_10_1016_j_coisb_2019_03_003 crossref_primary_10_1038_s41590_021_00910_8 crossref_primary_10_1371_journal_pbio_3003179 crossref_primary_10_1038_s41587_021_00989_2 crossref_primary_10_1186_s13058_022_01573_5 crossref_primary_10_3389_fimmu_2018_02298 crossref_primary_10_1038_s43587_021_00082_y crossref_primary_10_1038_s41598_017_11812_x crossref_primary_10_1038_s41380_022_01854_7 crossref_primary_10_1038_s41598_024_66059_0 crossref_primary_10_1080_2162402X_2018_1500106 crossref_primary_10_1172_JCI159579 crossref_primary_10_1371_journal_ppat_1009290 crossref_primary_10_1016_j_trim_2022_101652 crossref_primary_10_3389_fimmu_2019_01907 crossref_primary_10_1186_s13395_019_0196_z crossref_primary_10_1016_j_chom_2016_04_003 crossref_primary_10_1093_femsre_fuae011 crossref_primary_10_3389_fimmu_2021_741938 crossref_primary_10_1038_ni_3578 crossref_primary_10_1073_pnas_1713957115 crossref_primary_10_1007_s00335_018_9757_4 crossref_primary_10_1016_j_jri_2021_103307 crossref_primary_10_3389_fdata_2021_672460 crossref_primary_10_1177_19714009231163560 crossref_primary_10_3389_fonc_2023_1107532 crossref_primary_10_1073_pnas_1912008117 crossref_primary_10_7717_peerj_12570 crossref_primary_10_1007_s12013_025_01733_2 crossref_primary_10_1016_j_cell_2017_08_004 crossref_primary_10_1158_0008_5472_CAN_16_2346 crossref_primary_10_1093_nar_gkaf372 crossref_primary_10_1038_s41598_020_71144_1 crossref_primary_10_1016_j_immuni_2018_03_023 crossref_primary_10_1016_j_immuni_2021_07_009 crossref_primary_10_1371_journal_pone_0169271 crossref_primary_10_1182_blood_2020009309 crossref_primary_10_1002_JLB_MR0618_241RR crossref_primary_10_1016_j_jaci_2023_11_923 crossref_primary_10_1038_s41467_022_32782_3 crossref_primary_10_1126_science_aaf2807 crossref_primary_10_1126_sciimmunol_aai7677 crossref_primary_10_1016_j_mcn_2023_103852 crossref_primary_10_1158_0008_5472_CAN_17_3480 crossref_primary_10_1002_lt_25718 crossref_primary_10_1038_nrg_2016_67 crossref_primary_10_1016_j_csbj_2023_09_042 crossref_primary_10_4049_jimmunol_1800042 crossref_primary_10_1016_j_bbi_2018_11_008 crossref_primary_10_1016_j_ccell_2022_03_008 crossref_primary_10_1186_s12859_018_2486_6 crossref_primary_10_1111_imr_12817 crossref_primary_10_1016_j_csbj_2022_08_057 crossref_primary_10_1186_s12859_016_1012_y crossref_primary_10_1186_s13058_020_01362_y crossref_primary_10_1111_imr_12814 crossref_primary_10_4049_jimmunol_1700453 crossref_primary_10_1073_pnas_2000484117 crossref_primary_10_1158_2159_8290_CD_20_1661 crossref_primary_10_1084_jem_20190580 crossref_primary_10_3390_ijms23020821 crossref_primary_10_1016_j_ijrobp_2020_10_025 crossref_primary_10_1093_infdis_jiw446 crossref_primary_10_1016_j_cell_2020_05_007 crossref_primary_10_1016_j_ejca_2021_03_005 crossref_primary_10_1109_TCBB_2019_2931582 crossref_primary_10_1186_s12859_024_05899_z crossref_primary_10_1038_s41467_021_24584_w crossref_primary_10_1038_s43018_020_0066_y crossref_primary_10_3389_fonc_2020_00444 crossref_primary_10_1002_clt2_70081 crossref_primary_10_1016_j_jtho_2020_09_027 crossref_primary_10_3389_fimmu_2021_732006 crossref_primary_10_1002_advs_202505670 crossref_primary_10_1371_journal_pone_0158016 crossref_primary_10_3389_fmolb_2021_800721 crossref_primary_10_1038_s41598_019_49647_3 crossref_primary_10_3389_fgene_2016_00080 crossref_primary_10_3389_fimmu_2022_858246 crossref_primary_10_3389_fimmu_2022_942446 crossref_primary_10_12688_f1000research_10465_1 crossref_primary_10_1080_0886022X_2023_2202264 crossref_primary_10_1016_j_jtct_2021_02_023 crossref_primary_10_1182_blood_2022015451 crossref_primary_10_1126_science_abb9847 crossref_primary_10_1136_jitc_2020_000705 crossref_primary_10_1111_cea_13249 crossref_primary_10_1038_s41590_021_01060_7 crossref_primary_10_1111_cas_14795 crossref_primary_10_1038_s41467_024_49608_z crossref_primary_10_1038_s41408_023_00935_2 crossref_primary_10_1016_j_immuni_2019_12_007 crossref_primary_10_1038_s41590_018_0051_0 crossref_primary_10_1126_sciimmunol_abi4919 crossref_primary_10_1084_jem_20211191 crossref_primary_10_3389_fimmu_2021_690069 crossref_primary_10_1016_j_semcancer_2021_03_011 crossref_primary_10_1158_1541_7786_MCR_21_0560 crossref_primary_10_1016_j_cell_2021_03_056 crossref_primary_10_1186_s12859_017_1669_x crossref_primary_10_1016_j_bbi_2016_07_004 crossref_primary_10_1038_s41551_023_01091_5 crossref_primary_10_1016_j_ccell_2022_09_011 crossref_primary_10_1093_nar_gkx615 crossref_primary_10_4049_jimmunol_1900440 crossref_primary_10_1080_2162402X_2018_1525243 crossref_primary_10_1093_nargab_lqad081 crossref_primary_10_3389_fcell_2021_653357 crossref_primary_10_1038_nature17655 crossref_primary_10_1182_blood_2021014495 crossref_primary_10_1016_j_ygeno_2024_110870 crossref_primary_10_1186_s12859_020_03705_0 crossref_primary_10_1053_j_gastro_2019_07_028 crossref_primary_10_1371_journal_ppat_1009363 crossref_primary_10_1016_j_jtho_2019_08_008 crossref_primary_10_1038_s44161_022_00155_0 crossref_primary_10_1016_j_placenta_2021_06_011 crossref_primary_10_1038_s41467_025_61780_4 crossref_primary_10_1016_j_humgen_2025_201378 crossref_primary_10_1097_MD_0000000000035555 crossref_primary_10_1007_s13258_023_01407_4 crossref_primary_10_1038_s41590_021_01120_y crossref_primary_10_1002_1878_0261_13160 crossref_primary_10_1089_aid_2020_0061 crossref_primary_10_3389_fonc_2021_704531 crossref_primary_10_1126_scitranslmed_aaw4236 crossref_primary_10_1002_pbc_29582 crossref_primary_10_1093_nar_gky675 crossref_primary_10_1016_j_nbd_2023_106174 crossref_primary_10_1093_nar_gkx1040 crossref_primary_10_3389_fphys_2020_00621 crossref_primary_10_1155_2021_6648182 crossref_primary_10_1371_journal_ppat_1010867 crossref_primary_10_1038_s41523_021_00349_y crossref_primary_10_1096_fj_201902143R crossref_primary_10_1186_s12859_016_1403_0 crossref_primary_10_3389_fcvm_2022_1059543 crossref_primary_10_1016_j_immuni_2018_08_002 |
| ContentType | Journal Article |
| Copyright | Copyright © 2016 Elsevier Inc. All rights reserved. |
| Copyright_xml | – notice: Copyright © 2016 Elsevier Inc. All rights reserved. |
| DBID | CGR CUY CVF ECM EIF NPM 7X8 |
| DOI | 10.1016/j.immuni.2015.12.006 |
| 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 - Academic MEDLINE |
| 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 |
| Discipline | Medicine Biology |
| EISSN | 1097-4180 |
| EndPage | 206 |
| ExternalDocumentID | 26795250 |
| Genre | Research Support, Non-U.S. Gov't Journal Article Research Support, N.I.H., Extramural |
| GrantInformation_xml | – fundername: NIAID NIH HHS grantid: HHSN272201200028C – fundername: NCI NIH HHS grantid: U54 CA112962 – fundername: NIAID NIH HHS grantid: U19 AI090023 – fundername: NCI NIH HHS grantid: R01CA154480 – fundername: NCI NIH HHS grantid: R01 CA154480 – fundername: NCI NIH HHS grantid: R01 CA121941 – fundername: NIGMS NIH HHS grantid: R01GM074024 – fundername: NCI NIH HHS grantid: U24 CA194107 – fundername: NCI NIH HHS grantid: R01CA121941 – fundername: NIGMS NIH HHS grantid: R01 GM074024 |
| GroupedDBID | --- --K -DZ 0R~ 1RT 1~5 2WC 4.4 457 4G. 53G 5GY 62- 7-5 8FE 8FH AAEDT AAEDW AAKRW AALRI AAMRU AAVLU AAXUO AAYWO ABDGV ABJNI ABMAC ABOCM ACGFO ACGFS ACIWK ACPRK ACVFH ADBBV ADCNI ADEZE ADFRT ADVLN AEFWE AENEX AEUPX AEXQZ AFPUW AFRAH AFTJW AGCQF AGGSO AGKMS AHHHB AHMBA AIGII AITUG AKAPO AKBMS AKRWK AKYEP ALMA_UNASSIGNED_HOLDINGS AMRAJ APXCP ASPBG AVWKF AZFZN BAWUL BKEYQ BPHCQ BVXVI C45 CGR CS3 CUY CVF DIK DU5 E3Z EBS ECM EFKBS EIF EJD F5P FCP FDB FIRID IH2 IHE IXB J1W JIG LK8 LX5 M3Z M41 N9A NPM O-L O9- OK1 OVD P2P PQQKQ PROAC RIG ROL RPZ SCP SES SSZ TEORI TR2 7X8 |
| ID | FETCH-LOGICAL-c594t-63ba9b3ffc2a8858c649dae69e6910abb1fced3792ff10dbdd2ea2147e7584e52 |
| IEDL.DBID | 7X8 |
| ISICitedReferencesCount | 210 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000368347000023&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| IngestDate | Thu Oct 02 12:13:58 EDT 2025 Mon Jul 21 05:51:51 EDT 2025 |
| IsDoiOpenAccess | false |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 1 |
| Language | English |
| License | Copyright © 2016 Elsevier Inc. All rights reserved. |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c594t-63ba9b3ffc2a8858c649dae69e6910abb1fced3792ff10dbdd2ea2147e7584e52 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| OpenAccessLink | http://www.cell.com/article/S1074761315005324/pdf |
| PMID | 26795250 |
| PQID | 1760891098 |
| PQPubID | 23479 |
| PageCount | 13 |
| ParticipantIDs | proquest_miscellaneous_1760891098 pubmed_primary_26795250 |
| PublicationCentury | 2000 |
| PublicationDate | 2016-01-19 |
| PublicationDateYYYYMMDD | 2016-01-19 |
| PublicationDate_xml | – month: 01 year: 2016 text: 2016-01-19 day: 19 |
| PublicationDecade | 2010 |
| PublicationPlace | United States |
| PublicationPlace_xml | – name: United States |
| PublicationTitle | Immunity (Cambridge, Mass.) |
| PublicationTitleAlternate | Immunity |
| PublicationYear | 2016 |
| SSID | ssj0014590 |
| Score | 2.5934668 |
| Snippet | Gene-expression profiling has become a mainstay in immunology, but subtle changes in gene networks related to biological processes are hard to discern when... |
| SourceID | proquest pubmed |
| SourceType | Aggregation Database Index Database |
| StartPage | 194 |
| SubjectTerms | Animals Databases, Genetic Humans Inflammation - immunology Mice Species Specificity Transcriptome |
| Title | Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/26795250 https://www.proquest.com/docview/1760891098 |
| Volume | 44 |
| WOSCitedRecordID | wos000368347000023&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/eLvHCXMwpV3LS8MwGA_qVLz4mK_5IoLXYtImaXMSEYc7bAwfsFvJU3pYO-0m-N-bpB07CYJQ2lNKSL58z9-XHwA3qZCICeUiVWdeIyLckZIJIxG1iaQGJ4ZhEcgm0tEom0z4uE241S2scqkTg6LWlfI58lucMpQ528azu9lH5FmjfHW1pdBYB53EuTJeqtPJqopAKEfLdrmA6SpCz4UHdNGQBETsd8cyGJj-3n-ntg92W9cS3jeycADWTNkFWw3Z5HcXbA_bMvohmHotYEpdLKawsnDg52vgS_HeXPNZw6Z917ooGnpGT4-K1FCUGga6elNH4WsLBdvfw6KEzw3c1sB5BQeldaLWtEUegbf-4-vDU9TyLkSKcjKPWCIFl4m1KhZZRjPFCNfCMO4ejISU2Cqjk5TH1mKkpdaxEZ7vyLjggxgaH4ONsirNKYCIu8EUSyKwJQQZgSTnilKaxsrpEt0D18slzZ1c-2KFKE21qPPVovbASbMv-ay5gCOPWcp9OfbsD6PPwY7b7pA1wfwCdKw71eYSbKqveVF_XgWBce_RePgDrxTOCg |
| 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=Compendium+of+Immune+Signatures+Identifies+Conserved+and+Species-Specific+Biology+in+Response+to+Inflammation&rft.jtitle=Immunity+%28Cambridge%2C+Mass.%29&rft.au=Godec%2C+Jernej&rft.au=Tan%2C+Yan&rft.au=Liberzon%2C+Arthur&rft.au=Tamayo%2C+Pablo&rft.date=2016-01-19&rft.eissn=1097-4180&rft.volume=44&rft.issue=1&rft.spage=194&rft.epage=206&rft_id=info:doi/10.1016%2Fj.immuni.2015.12.006&rft.externalDBID=NO_FULL_TEXT |