Literature DB >> 30478325

Interpretation of an individual functional genomics experiment guided by massive public data.

Young-Suk Lee1,2,3, Aaron K Wong4, Alicja Tadych1, Boris M Hartmann5, Christopher Y Park4, Veronica A DeJesus6, Irene Ramos6, Elena Zaslavsky7, Stuart C Sealfon8, Olga G Troyanskaya1,2,4.   

Abstract

A key unmet challenge in interpreting omics experiments is inferring biological meaning in the context of public functional genomics data. We developed a computational framework, Your Evidence Tailored Integration (YETI; http://yeti.princeton.edu/ ), which creates specialized functional interaction maps from large public datasets relevant to an individual omics experiment. Using this tailored integration, we predicted and experimentally confirmed an unexpected divergence in viral replication after seasonal or pandemic human influenza virus infection.

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Year:  2018        PMID: 30478325      PMCID: PMC6941785          DOI: 10.1038/s41592-018-0218-5

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  40 in total

1.  The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals.

Authors:  Masaaki Kotera; Mika Hirakawa; Toshiaki Tokimatsu; Susumu Goto; Minoru Kanehisa
Journal:  Methods Mol Biol       Date:  2012

Review 2.  Advantages and limitations of current network inference methods.

Authors:  Riet De Smet; Kathleen Marchal
Journal:  Nat Rev Microbiol       Date:  2010-08-31       Impact factor: 60.633

3.  The distinctive features of influenza virus infection of dendritic cells.

Authors:  A Bender; M Albert; A Reddy; M Feldman; B Sauter; G Kaplan; W Hellman; N Bhardwaj
Journal:  Immunobiology       Date:  1998-03       Impact factor: 3.144

4.  The Gene Expression Omnibus Database.

Authors:  Emily Clough; Tanya Barrett
Journal:  Methods Mol Biol       Date:  2016

5.  The MIPS mammalian protein-protein interaction database.

Authors:  Philipp Pagel; Stefan Kovac; Matthias Oesterheld; Barbara Brauner; Irmtraud Dunger-Kaltenbach; Goar Frishman; Corinna Montrone; Pekka Mark; Volker Stümpflen; Hans-Werner Mewes; Andreas Ruepp; Dmitrij Frishman
Journal:  Bioinformatics       Date:  2004-11-05       Impact factor: 6.937

6.  FIMO: scanning for occurrences of a given motif.

Authors:  Charles E Grant; Timothy L Bailey; William Stafford Noble
Journal:  Bioinformatics       Date:  2011-02-16       Impact factor: 6.937

7.  Finding function: evaluation methods for functional genomic data.

Authors:  Chad L Myers; Daniel R Barrett; Matthew A Hibbs; Curtis Huttenhower; Olga G Troyanskaya
Journal:  BMC Genomics       Date:  2006-07-25       Impact factor: 3.969

8.  Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.

Authors:  Christopher Y Park; Aaron K Wong; Casey S Greene; Jessica Rowland; Yuanfang Guan; Lars A Bongo; Rebecca D Burdine; Olga G Troyanskaya
Journal:  PLoS Comput Biol       Date:  2013-03-14       Impact factor: 4.475

9.  Comparison of co-expression measures: mutual information, correlation, and model based indices.

Authors:  Lin Song; Peter Langfelder; Steve Horvath
Journal:  BMC Bioinformatics       Date:  2012-12-09       Impact factor: 3.169

10.  Understanding multicellular function and disease with human tissue-specific networks.

Authors:  Casey S Greene; Arjun Krishnan; Aaron K Wong; Emanuela Ricciotti; Rene A Zelaya; Daniel S Himmelstein; Ran Zhang; Boris M Hartmann; Elena Zaslavsky; Stuart C Sealfon; Daniel I Chasman; Garret A FitzGerald; Kara Dolinski; Tilo Grosser; Olga G Troyanskaya
Journal:  Nat Genet       Date:  2015-04-27       Impact factor: 38.330

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  1 in total

1.  An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis.

Authors:  Guanjue Xiang; Cheryl A Keller; Elisabeth Heuston; Belinda M Giardine; Lin An; Alexander Q Wixom; Amber Miller; April Cockburn; Michael E G Sauria; Kathryn Weaver; Jens Lichtenberg; Berthold Göttgens; Qunhua Li; David Bodine; Shaun Mahony; James Taylor; Gerd A Blobel; Mitchell J Weiss; Yong Cheng; Feng Yue; Jim Hughes; Douglas R Higgs; Yu Zhang; Ross C Hardison
Journal:  Genome Res       Date:  2020-03-04       Impact factor: 9.043

  1 in total

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