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Items: 1 to 20 of 24

1.

ProbCD: enrichment analysis accounting for categorization uncertainty.

Vêncio RZ, Shmulevich I.

BMC Bioinformatics. 2007 Oct 12;8:383.

2.

Enrichment or depletion of a GO category within a class of genes: which test?

Rivals I, Personnaz L, Taing L, Potier MC.

Bioinformatics. 2007 Feb 15;23(4):401-7. Epub 2006 Dec 20.

PMID:
17182697
3.

Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments.

Sartor MA, Tomlinson CR, Wesselkamper SC, Sivaganesan S, Leikauf GD, Medvedovic M.

BMC Bioinformatics. 2006 Dec 19;7:538.

4.

BayGO: Bayesian analysis of ontology term enrichment in microarray data.

Vêncio RZ, Koide T, Gomes SL, Pereira CA.

BMC Bioinformatics. 2006 Feb 23;7:86.

5.

Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis.

Sotiriou C, Wirapati P, Loi S, Harris A, Fox S, Smeds J, Nordgren H, Farmer P, Praz V, Haibe-Kains B, Desmedt C, Larsimont D, Cardoso F, Peterse H, Nuyten D, Buyse M, Van de Vijver MJ, Bergh J, Piccart M, Delorenzi M.

J Natl Cancer Inst. 2006 Feb 15;98(4):262-72.

PMID:
16478745
6.

From genomics to chemical genomics: new developments in KEGG.

Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D354-7.

7.

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP.

Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50. Epub 2005 Sep 30.

8.

Discovering statistically significant pathways in expression profiling studies.

Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJ.

Proc Natl Acad Sci U S A. 2005 Sep 20;102(38):13544-9. Epub 2005 Sep 8.

9.

An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival.

Miller LD, Smeds J, George J, Vega VB, Vergara L, Ploner A, Pawitan Y, Hall P, Klaar S, Liu ET, Bergh J.

Proc Natl Acad Sci U S A. 2005 Sep 20;102(38):13550-5. Epub 2005 Sep 2. Erratum in: Proc Natl Acad Sci U S A. 2005 Dec 6;102(49):17882.

10.

Up-regulation and profibrotic role of osteopontin in human idiopathic pulmonary fibrosis.

Pardo A, Gibson K, Cisneros J, Richards TJ, Yang Y, Becerril C, Yousem S, Herrera I, Ruiz V, Selman M, Kaminski N.

PLoS Med. 2005 Sep;2(9):e251. Epub 2005 Sep 6.

11.

High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID).

Zeeberg BR, Qin H, Narasimhan S, Sunshine M, Cao H, Kane DW, Reimers M, Stephens RM, Bryant D, Burt SK, Elnekave E, Hari DM, Wynn TA, Cunningham-Rundles C, Stewart DM, Nelson D, Weinstein JN.

BMC Bioinformatics. 2005 Jul 5;6:168.

12.

Ontological analysis of gene expression data: current tools, limitations, and open problems.

Khatri P, Drăghici S.

Bioinformatics. 2005 Sep 15;21(18):3587-95. Epub 2005 Jun 30.

13.

Recent additions and improvements to the Onto-Tools.

Khatri P, Sellamuthu S, Malhotra P, Amin K, Done A, Draghici S.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W762-5.

14.

Effects of threshold choice on biological conclusions reached during analysis of gene expression by DNA microarrays.

Pan KH, Lih CJ, Cohen SN.

Proc Natl Acad Sci U S A. 2005 Jun 21;102(25):8961-5. Epub 2005 Jun 10.

15.

Pathways to the analysis of microarray data.

Curtis RK, Oresic M, Vidal-Puig A.

Trends Biotechnol. 2005 Aug;23(8):429-35. Review.

PMID:
15950303
16.

The Gene Ontology (GO) database and informatics resource.

Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R; Gene Ontology Consortium.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61.

17.

Characterizing gene sets with FuncAssociate.

Berriz GF, King OD, Bryant B, Sander C, Roth FP.

Bioinformatics. 2003 Dec 12;19(18):2502-4.

PMID:
14668247
18.

Identifying biological themes within lists of genes with EASE.

Hosack DA, Dennis G Jr, Sherman BT, Lane HC, Lempicki RA.

Genome Biol. 2003;4(10):R70. Epub 2003 Sep 11.

19.

Statistical significance for genomewide studies.

Storey JD, Tibshirani R.

Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9440-5. Epub 2003 Jul 25.

20.

DAVID: Database for Annotation, Visualization, and Integrated Discovery.

Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA.

Genome Biol. 2003;4(5):P3. Epub 2003 Apr 3.

PMID:
12734009

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