Ashish Jain1,2, Geetu Tuteja1,2. 1. Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA. 2. Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.
Abstract
SUMMARY: RNA-Seq data analysis results in lists of genes that may have a similar function, based on differential gene expression analysis or co-expression network analysis. While tools have been developed to identify biological processes that are enriched in the genes sets, there remains a need for tools that identify enrichment of tissue-specific genes. Therefore, we developed TissueEnrich, a tool that calculates tissue-specific gene enrichment in an input gene set. We demonstrated that TissueEnrich can assign tissue identities to single cell clusters and differentiated embryonic stem cells. AVAILABILITY AND IMPLEMENTATION: The TissueEnrich web application is freely available at http://tissueenrich.gdcb.iastate.edu/. The R package is available through Bioconductor at https://bioconductor.org/packages/TissueEnrich. Both the web application and R package are for non-profit academic use under the MIT license. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: RNA-Seq data analysis results in lists of genes that may have a similar function, based on differential gene expression analysis or co-expression network analysis. While tools have been developed to identify biological processes that are enriched in the genes sets, there remains a need for tools that identify enrichment of tissue-specific genes. Therefore, we developed TissueEnrich, a tool that calculates tissue-specific gene enrichment in an input gene set. We demonstrated that TissueEnrich can assign tissue identities to single cell clusters and differentiated embryonic stem cells. AVAILABILITY AND IMPLEMENTATION: The TissueEnrich web application is freely available at http://tissueenrich.gdcb.iastate.edu/. The R package is available through Bioconductor at https://bioconductor.org/packages/TissueEnrich. Both the web application and R package are for non-profit academic use under the MIT license. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Shinichiro Yabe; Andrei P Alexenko; Mitsuyoshi Amita; Ying Yang; Danny J Schust; Yoel Sadovsky; Toshihiko Ezashi; R Michael Roberts Journal: Proc Natl Acad Sci U S A Date: 2016-04-05 Impact factor: 11.205
Authors: Mathias Uhlén; Linn Fagerberg; Björn M Hallström; Cecilia Lindskog; Per Oksvold; Adil Mardinoglu; Åsa Sivertsson; Caroline Kampf; Evelina Sjöstedt; Anna Asplund; IngMarie Olsson; Karolina Edlund; Emma Lundberg; Sanjay Navani; Cristina Al-Khalili Szigyarto; Jacob Odeberg; Dijana Djureinovic; Jenny Ottosson Takanen; Sophia Hober; Tove Alm; Per-Henrik Edqvist; Holger Berling; Hanna Tegel; Jan Mulder; Johan Rockberg; Peter Nilsson; Jochen M Schwenk; Marica Hamsten; Kalle von Feilitzen; Mattias Forsberg; Lukas Persson; Fredric Johansson; Martin Zwahlen; Gunnar von Heijne; Jens Nielsen; Fredrik Pontén Journal: Science Date: 2015-01-23 Impact factor: 47.728
Authors: Linda Szabo; Robert Morey; Nathan J Palpant; Peter L Wang; Nastaran Afari; Chuan Jiang; Mana M Parast; Charles E Murry; Louise C Laurent; Julia Salzman Journal: Genome Biol Date: 2015-06-16 Impact factor: 13.583
Authors: Antonio Scialdone; Yosuke Tanaka; Wajid Jawaid; Victoria Moignard; Nicola K Wilson; Iain C Macaulay; John C Marioni; Berthold Göttgens Journal: Nature Date: 2016-07-06 Impact factor: 49.962
Authors: Jiude Mao; Ashish Jain; Nancy D Denslow; Mohammad-Zaman Nouri; Sixue Chen; Tingting Wang; Ning Zhu; Jin Koh; Saurav J Sarma; Barbara W Sumner; Zhentian Lei; Lloyd W Sumner; Nathan J Bivens; R Michael Roberts; Geetu Tuteja; Cheryl S Rosenfeld Journal: Proc Natl Acad Sci U S A Date: 2020-02-18 Impact factor: 11.205
Authors: Francisco Requena; Hamza Hadj Abdallah; Alejandro García; Patrick Nitschké; Sergi Romana; Valérie Malan; Antonio Rausell Journal: Nucleic Acids Res Date: 2021-07-02 Impact factor: 16.971
Authors: Zhongyi Hu; Jiao Yuan; Meixiao Long; Junjie Jiang; Youyou Zhang; Tianli Zhang; Mu Xu; Yi Fan; Janos L Tanyi; Kathleen T Montone; Omid Tavana; Ho Man Chan; Xiaowen Hu; Robert H Vonderheide; Lin Zhang Journal: Nat Cancer Date: 2021-12-13
Authors: Daojun Yuan; Corrinne E Grover; Guanjing Hu; Mengqiao Pan; Emma R Miller; Justin L Conover; Spencer P Hunt; Joshua A Udall; Jonathan F Wendel Journal: Adv Sci (Weinh) Date: 2021-03-15 Impact factor: 16.806