Literature DB >> 14519205

Identifying biological themes within lists of genes with EASE.

Douglas A Hosack1, Glynn Dennis, Brad T Sherman, H Clifford Lane, Richard A Lempicki.   

Abstract

EASE is a customizable software application for rapid biological interpretation of gene lists that result from the analysis of microarray, proteomics, SAGE and other high-throughput genomic data. The biological themes returned by EASE recapitulate manually determined themes in previously published gene lists and are robust to varying methods of normalization, intensity calculation and statistical selection of genes. EASE is a powerful tool for rapidly converting the results of functional genomics studies from 'genes' to 'themes'.

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Mesh：

Year:  2003        PMID： 14519205      PMCID： PMC328459          DOI： 10.1186/gb-2003-4-10-r70

Source DB:  PubMed          Journal:  Genome Biol        ISSN： 1474-7596            Impact factor:   13.583


  26 in total

1.  Influences of aging and caloric restriction on the transcriptional profile of skeletal muscle from rhesus monkeys.

Authors:  T Kayo; D B Allison; R Weindruch; T A Prolla
Journal:  Proc Natl Acad Sci U S A       Date:  2001-04-17       Impact factor: 11.205

2.  Significance analysis of microarrays applied to the ionizing radiation response.

Authors:  V G Tusher; R Tibshirani; G Chu
Journal:  Proc Natl Acad Sci U S A       Date:  2001-04-17       Impact factor: 11.205

3.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

4.  Introducing RefSeq and LocusLink: curated human genome resources at the NCBI.

Authors:  K D Pruitt; K S Katz; H Sicotte; D R Maglott
Journal:  Trends Genet       Date:  2000-01       Impact factor: 11.639

5.  The KEGG databases at GenomeNet.

Authors:  Minoru Kanehisa; Susumu Goto; Shuichi Kawashima; Akihiro Nakaya
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

6.  The Protein Information Resource: an integrated public resource of functional annotation of proteins.

Authors:  Cathy H Wu; Hongzhan Huang; Leslie Arminski; Jorge Castro-Alvear; Yongxing Chen; Zhang-Zhi Hu; Robert S Ledley; Kali C Lewis; Hans-Werner Mewes; Bruce C Orcutt; Baris E Suzek; Akira Tsugita; C R Vinayaka; Lai-Su L Yeh; Jian Zhang; Winona C Barker
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

7.  GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways.

Authors:  Kam D Dahlquist; Nathan Salomonis; Karen Vranizan; Steven C Lawlor; Bruce R Conklin
Journal:  Nat Genet       Date:  2002-05       Impact factor: 38.330

8.  HIV envelope induces a cascade of cell signals in non-proliferating target cells that favor virus replication.

Authors:  Claudia Cicala; James Arthos; Sara M Selig; Glynn Dennis; Douglas A Hosack; Donald Van Ryk; Marion L Spangler; Tavis D Steenbeke; Prateeti Khazanie; Neil Gupta; Jun Yang; Marybeth Daucher; Richard A Lempicki; Anthony S Fauci
Journal:  Proc Natl Acad Sci U S A       Date:  2002-06-27       Impact factor: 11.205

9.  The Pfam protein families database.

Authors:  Alex Bateman; Ewan Birney; Lorenzo Cerruti; Richard Durbin; Laurence Etwiller; Sean R Eddy; Sam Griffiths-Jones; Kevin L Howe; Mhairi Marshall; Erik L L Sonnhammer
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

10.  Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection.

Authors:  C Li; W H Wong
Journal:  Proc Natl Acad Sci U S A       Date:  2001-01-02       Impact factor: 11.205
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  852 in total

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Authors:  Samir Satih; Nasséra Chalabi; Nadège Rabiau; Rémy Bosviel; Luc Fontana; Yves-Jean Bignon; Dominique J Bernard-Gallon
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3.  Effects of cryopreservation on the transcriptome of human embryonic stem cells after thawing and culturing.

Authors:  Vilas Wagh; Kesavan Meganathan; Smita Jagtap; John Antonydas Gaspar; Johannes Winkler; Dimitry Spitkovsky; Jürgen Hescheler; Agapios Sachinidis
Journal:  Stem Cell Rev Rep       Date:  2011-09       Impact factor: 5.739

4.  Identification of the transcriptional targets of FOXP2, a gene linked to speech and language, in developing human brain.

Authors:  Elizabeth Spiteri; Genevieve Konopka; Giovanni Coppola; Jamee Bomar; Michael Oldham; Jing Ou; Sonja C Vernes; Simon E Fisher; Bing Ren; Daniel H Geschwind
Journal:  Am J Hum Genet       Date:  2007-10-31       Impact factor: 11.025

5.  A Bayesian extension of the hypergeometric test for functional enrichment analysis.

Authors:  Jing Cao; Song Zhang
Journal:  Biometrics       Date:  2013-12-09       Impact factor: 2.571

6.  Identification of modulated genes by three classes of chemopreventive agents at preneoplastic stages in a p53-null mouse mammary tumor model.

Authors:  Martín C Abba; Yuhui Hu; Carla C Levy; Sally Gaddis; Frances S Kittrell; Jamal Hill; Reid P Bissonnette; Powel H Brown; Daniel Medina; C Marcelo Aldaz
Journal:  Cancer Prev Res (Phila)       Date:  2009-01-27

7.  Gene expression profiling of granulosa cells from PCOS patients following varying doses of human chorionic gonadotropin.

Authors:  Serdar Coskun; Hasan H Otu; Khalid A Awartani; Laila A Al-Alwan; Saad Al-Hassan; Hend Al-Mayman; Namik Kaya; Mehmet S Inan
Journal:  J Assist Reprod Genet       Date:  2013-02-05       Impact factor: 3.412

8.  Acute appendicitis is characterized by a uniform and highly selective pattern of inflammatory gene expression.

Authors:  C G Murphy; J N Glickman; K Tomczak; Y Y Wang; A H Beggs; M W Shannon; B H Horwitz
Journal:  Mucosal Immunol       Date:  2008-07       Impact factor: 7.313

9.  Celsius: a community resource for Affymetrix microarray data.

Authors:  Allen Day; Marc R J Carlson; Jun Dong; Brian D O'Connor; Stanley F Nelson
Journal:  Genome Biol       Date:  2007       Impact factor: 13.583

10.  Expression microarray analysis implicates apoptosis and interferon-responsive mechanisms in susceptibility to experimental cerebral malaria.

Authors:  Fiona E Lovegrove; Sina A Gharib; Samir N Patel; Cheryl A Hawkes; Kevin C Kain; W Conrad Liles
Journal:  Am J Pathol       Date:  2007-11-08       Impact factor: 4.307
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