Transfer of regulatory knowledge from human to mouse for functional genomics analysis
Transcriptome profiling followed by differential gene expression analysis often leads to lists of genes that are hard to analyze and interpret. Functional genomics tools are powerful approaches for downstream analysis, as they summarize the large and noisy gene expression space into a smaller number...
Gespeichert in:
| Hauptverfasser: | , , |
|---|---|
| Dokumenttyp: | Article (Journal) |
| Sprache: | Englisch |
| Veröffentlicht: |
2020
|
| In: |
Biochimica et biophysica acta. Gene regulatory mechanisms
Year: 2020, Jahrgang: 1863, Heft: 6 |
| ISSN: | 1876-4320 |
| DOI: | 10.1016/j.bbagrm.2019.194431 |
| Online-Zugang: | Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1016/j.bbagrm.2019.194431
|
| Verfasserangaben: | Christian H. Holland, Bence Szalai, Julio Saez-Rodriguez |
MARC
| LEADER | 00000caa a2200000 c 4500 | ||
|---|---|---|---|
| 001 | 1699797374 | ||
| 003 | DE-627 | ||
| 005 | 20220818112535.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 200604s2020 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1016/j.bbagrm.2019.194431 |2 doi | |
| 035 | |a (DE-627)1699797374 | ||
| 035 | |a (DE-599)KXP1699797374 | ||
| 035 | |a (OCoLC)1341328468 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rda | ||
| 041 | |a eng | ||
| 084 | |a 33 |2 sdnb | ||
| 100 | 1 | |a Holland, Christian H. |d 1991- |e VerfasserIn |0 (DE-588)1203164831 |0 (DE-627)1687980101 |4 aut | |
| 245 | 1 | 0 | |a Transfer of regulatory knowledge from human to mouse for functional genomics analysis |c Christian H. Holland, Bence Szalai, Julio Saez-Rodriguez |
| 264 | 1 | |c 2020 | |
| 300 | |a 8 | ||
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a Computermedien |b c |2 rdamedia | ||
| 338 | |a Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Available online: 13 September 2019 | ||
| 500 | |a Gesehen am 04.06.2020 | ||
| 520 | |a Transcriptome profiling followed by differential gene expression analysis often leads to lists of genes that are hard to analyze and interpret. Functional genomics tools are powerful approaches for downstream analysis, as they summarize the large and noisy gene expression space into a smaller number of biological meaningful features. In particular, methods that estimate the activity of processes by mapping transcripts level to process members are popular. However, footprints of either a pathway or transcription factor (TF) on gene expression show superior performance over mapping-based gene sets. These footprints are largely developed for humans and their usability in the broadly-used model organism Mus musculus is uncertain. Evolutionary conservation of the gene regulatory system suggests that footprints of human pathways and TFs can functionally characterize mice data. In this paper we analyze this hypothesis. We perform a comprehensive benchmark study exploiting two state-of-the-art footprint methods, DoRothEA and an extended version of PROGENy. These methods infer TF and pathway activity, respectively. Our results show that both can recover mouse perturbations, confirming our hypothesis that footprints are conserved between mice and humans. Subsequently, we illustrate the usability of PROGENy and DoRothEA by recovering pathway/TF-disease associations from newly generated disease sets. Additionally, we provide pathway and TF activity scores for a large collection of human and mouse perturbation and disease experiments (2374). We believe that this resource, available for interactive exploration and download (https://saezlab.shinyapps.io/footprint_scores/), can have broad applications including the study of diseases and therapeutics. | ||
| 650 | 4 | |a cancer | |
| 650 | 4 | |a datasets | |
| 650 | 4 | |a expression | |
| 650 | 4 | |a Functional genomics | |
| 650 | 4 | |a Pathway activity | |
| 650 | 4 | |a Signaling footprints | |
| 650 | 4 | |a Transcription factor activity | |
| 700 | 1 | |a Szalai, Bence |e VerfasserIn |0 (DE-588)1204151032 |0 (DE-627)1689296461 |4 aut | |
| 700 | 1 | |a Sáez Rodríguez, Julio |d 1978- |e VerfasserIn |0 (DE-588)133764362 |0 (DE-627)555766632 |0 (DE-576)300083114 |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Biochimica et biophysica acta. Gene regulatory mechanisms |d Amsterdam [u.a.] : Elsevier, 2008 |g 1863(2020,6) Artikel-Nummer 194431, 8 Seiten |w (DE-627)557882168 |w (DE-600)2406725-8 |w (DE-576)27798128X |x 1876-4320 |7 nnas |a Transfer of regulatory knowledge from human to mouse for functional genomics analysis |
| 773 | 1 | 8 | |g volume:1863 |g year:2020 |g number:6 |g extent:8 |a Transfer of regulatory knowledge from human to mouse for functional genomics analysis |
| 856 | 4 | 0 | |u https://doi.org/10.1016/j.bbagrm.2019.194431 |x Verlag |x Resolving-System |z lizenzpflichtig |3 Volltext |
| 951 | |a AR | ||
| 992 | |a 20200604 | ||
| 993 | |a Article | ||
| 994 | |a 2020 | ||
| 998 | |g 133764362 |a Sáez Rodríguez, Julio |m 133764362:Sáez Rodríguez, Julio |d 700000 |d 716000 |d 910000 |d 912900 |e 700000PS133764362 |e 716000PS133764362 |e 910000PS133764362 |e 912900PS133764362 |k 0/700000/ |k 1/700000/716000/ |k 0/910000/ |k 1/910000/912900/ |p 3 |y j | ||
| 998 | |g 1203164831 |a Holland, Christian H. |m 1203164831:Holland, Christian H. |d 50000 |d 700000 |d 716000 |e 50000PH1203164831 |e 700000PH1203164831 |e 716000PH1203164831 |k 0/50000/ |k 0/700000/ |k 1/700000/716000/ |p 1 |x j | ||
| 999 | |a KXP-PPN1699797374 |e 3682603425 | ||
| BIB | |a Y | ||
| SER | |a journal | ||
| JSO | |a {"id":{"eki":["1699797374"],"doi":["10.1016/j.bbagrm.2019.194431"]},"recId":"1699797374","relHost":[{"recId":"557882168","id":{"issn":["1876-4320"],"zdb":["2406725-8"],"eki":["557882168"]},"title":[{"partname":"Gene regulatory mechanisms","subtitle":"BBA","title_sort":"Biochimica et biophysica acta","title":"Biochimica et biophysica acta"}],"note":["Gesehen am 08.01.2020","Bis 2016 Bände zugleich Bände von: Biochimica et biophysica acta"],"origin":[{"publisherPlace":"Amsterdam [u.a.]","dateIssuedKey":"2008","publisher":"Elsevier","dateIssuedDisp":"2008-"}],"pubHistory":["1779.2008 -"],"disp":"Transfer of regulatory knowledge from human to mouse for functional genomics analysisBiochimica et biophysica acta. Gene regulatory mechanisms","type":{"media":"Online-Ressource","bibl":"periodical"},"language":["eng"],"titleAlt":[{"title":"Biochimica et biophysica acta / Gene regulatory mechanisms"},{"title":"BBA gene regulatory mechanisms"}],"part":{"year":"2020","volume":"1863","text":"1863(2020,6) Artikel-Nummer 194431, 8 Seiten","extent":"8","issue":"6"}}],"physDesc":[{"extent":"8 S."}],"name":{"displayForm":["Christian H. Holland, Bence Szalai, Julio Saez-Rodriguez"]},"type":{"bibl":"article-journal","media":"Online-Ressource"},"title":[{"title":"Transfer of regulatory knowledge from human to mouse for functional genomics analysis","title_sort":"Transfer of regulatory knowledge from human to mouse for functional genomics analysis"}],"note":["Available online: 13 September 2019","Gesehen am 04.06.2020"],"origin":[{"dateIssuedDisp":"2020","dateIssuedKey":"2020"}],"language":["eng"],"person":[{"display":"Holland, Christian H.","family":"Holland","given":"Christian H.","role":"aut"},{"family":"Szalai","display":"Szalai, Bence","given":"Bence","role":"aut"},{"family":"Sáez Rodríguez","display":"Sáez Rodríguez, Julio","given":"Julio","role":"aut"}]} | ||
| SRT | |a HOLLANDCHRTRANSFEROF2020 | ||