Group: BioinfoCIPF - with tag functional_annotation [43 articles]

DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis

BMC Bioinformatics, Vol. 8 (02 November 2007), 426.

by Brad T Sherman, Da W Huang, Qina Tan, Yongjian Guo, Stephan Bour, David Liu, Robert Stephens, Michael W Baseler, Clifford H Lane, Richard A Lempicki

posted to database expression functional_annotation microarray by ealloza to the group BioinfoCIPF on 2007-11-05 17:30:43 as along with 4 people hpaces jyuh jfr barriot

GENECODIS: A web-based tool for finding significant concurrent annotations in gene lists

Genome Biology, Vol. 8 (04 January 2007), R3.

by Pedro Carmona-Saez, Monica Chagoyen, Francisco Tirado, Jose M Carazo, Alberto Pascual-Montano

posted to functional_annotation gene_list_analysis suite by ealloza to the group BioinfoCIPF on 2007-10-25 16:26:30 as along with 3 people yas aalibes jfr

Chromosomal Microdeletions and Genes Functions: A cluster of chromosomal microdeletions and the deleted genes functions

European Journal of Human Genetics, Vol. aop, No. current.

by Ruti Parvari, Eli Hershkovitz

posted to aberration chromosome disease functional_annotation rearrangement by ealloza to the group BioinfoCIPF on 2007-10-02 17:32:06 as

EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species

BMC Genomics, Vol. 8 (24 July 2007), 246.

by Xin Zhou, Zhen Su

posted to gene_set_analysis functional_annotation by ealloza to the group BioinfoCIPF on 2007-07-30 12:40:38 as along with 1 person sgoetz

THE EVOLUTIONARY DYNAMICS OF EUKARYOTIC GENE ORDER

Nat Rev Genet, Vol. 5, No. 4. (April 2004), pp. 299-310.

by Laurence D Hurst, Csaba Pal, Martin J Lercher

posted to review gene_order functional_annotation by ealloza to the group BioinfoCIPF on 2007-06-13 11:56:04 as

Locational distribution of gene functional classes in Arabidopsis thaliana

BMC Bioinformatics, Vol. 8, No. 1. (2007)

by Michael Riley, Amanda Clare, Ross King

posted to gene_order functional_annotation arabidopsis by ealloza to the group BioinfoCIPF on 2007-04-17 18:30:26 as along with 1 person big_bull_000

GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms.

Bioinformatics, Vol. 20, No. 16. (1 November 2004), pp. 2618-2625.

by M Smid, LC Dorssers

posted to algorithm expression functional_annotation gene_set_analysis microarray sage by ealloza to the group BioinfoCIPF on 2007-03-12 15:40:07 as

GOAL: automated Gene Ontology analysis of expression profiles.

Nucleic Acids Res, Vol. 32, No. Web Server issue. (1 July 2004)

by S Volinia, R Evangelisti, F Francioso, D Arcelli, M Carella, P Gasparini

posted to algorithm expression functional_annotation gene_set_analysis microarray sage by ealloza to the group BioinfoCIPF on 2007-03-12 15:38:46 as

Identifying subtle interrelated changes in functional gene categories using continuous measures of gene expression.

Bioinformatics, Vol. 21, No. 7. (1 April 2005), pp. 1129-1137.

by Y Ben-Shaul, H Bergman, H Soreq

posted to algorithm expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2007-03-12 15:36:36 as

GenePattern 2.0

Nature Genetics, Vol. 38, No. 5., pp. 500-501.

by Michael Reich, Ted Liefeld, Joshua Gould, Jim Lerner, Pablo Tamayo, Jill P Mesirov

posted to algorithm expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2007-03-12 15:06:29 as along with 3 people jyuh rdiaz mayercd

Discovering statistically significant pathways in expression profiling studies.

Proc Natl Acad Sci U S A, Vol. 102, No. 38. (20 September 2005), pp. 13544-13549.

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

posted to algorithm expression functional_annotation gene_set_analysis microarray permutations by ealloza to the group BioinfoCIPF on 2007-03-12 15:03:34 as along with 7 people giovenko heliopais srp33 dragonrez maryee frohike justescaped

A global test for groups of genes: testing association with a clinical outcome.

Bioinformatics, Vol. 20, No. 1. (1 January 2004), pp. 93-99.

by JJ Goeman, SA van de Geer, F de Kort, HC van Houwelingen

posted to algorithm expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2007-03-12 14:43:58 as along with 2 people dragonrez ugengma

Analyzing gene expression data in terms of gene sets: methodological issues.

Bioinformatics (15 February 2007)

by Jelle J J Goeman, Peter Bühlmann

posted to algorithm comparison expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2007-03-12 14:39:32 as along with 5 people and 1 group diging_data jyuh heliopais jfr shigepong BTS-PT-AS-CS

Computational prediction of cancer-gene function

Nature Reviews Cancer, Vol. 7, No. 1. (14 December 2006), pp. 23-34.

by Pingzhao Hu, Gary Bader, Dennis A Wigle, Andrew Emili

posted to cancer computational functional_annotation ontology prediction review by ealloza to the group BioinfoCIPF on 2007-02-15 15:33:31 as along with 6 people srp33 jyuh jfr emb51 Garamonfok cerami

Discovering tightly regulated and differentially expressed gene sets in whole genome expression data.

Bioinformatics, Vol. 23, No. 2. (15 January 2007)

by C Ye, E Eskin

posted to microarray gene_set_analysis functional_annotation expression algorithm by ealloza to the group BioinfoCIPF on 2007-01-24 12:44:19 as along with 2 people and 1 group shigepong MrBrownShoes NBI

A scalable method for integration and functional analysis of multiple microarray data sets.

Bioinformatics (27 September 2006)

by Curtis Huttenhower, Matt Hibbs, Chad Myers, Olga G G Troyanskaya

posted to platform microarray meta_analysis functional_annotation expression bayes by ealloza to the group BioinfoCIPF on 2006-11-06 16:44:34 as along with 1 person macavity1g

GOLEM: an interactive graph-based gene-ontology navigation and analysis tool

BMC Bioinformatics, Vol. 7 (10 October 2006), 443.

by Rachel SG Sealfon, Matthew A Hibbs, Curtis Huttenhower, Chad L Myers, Olga G Troyanskaya

posted to functional_annotation gene_list_analysis ontology visualisation by ealloza to the group BioinfoCIPF on 2006-10-16 12:32:39 as along with 5 people and 1 group carlk jyuh tardigrade giovanni jdiggans GeschwindLab

Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data

BMC Bioinformatics, Vol. 7 (03 October 2006), 426.

by Alex Lewin, Ian C Grieve

posted to ontology microarray gene_list_analysis functional_annotation expression composite by ealloza to the group BioinfoCIPF on 2006-10-05 11:24:23 as along with 6 people and 1 group ndiaz giovanni jdiggans uprock heliopais waghsk GeschwindLab

ADGO: analysis of differentially expressed gene sets using composite GO annotation

Bioinformatics, Vol. 22, No. 18. (15 September 2006), pp. 2249-2253.

by Dougu Nam, Sang-Bae Kim, Seon-Kyu Kim, Sungjin Yang, Seon-Young Kim, In-Sun Chu

posted to composite expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2006-09-07 12:19:17 as along with 2 people jdiggans heliopais

Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes

BMC Bioinformatics, Vol. 7 (31 August 2006), 397.

by Susmita Datta, Somnath Datta

posted to clustering functional_annotation by ealloza to the group BioinfoCIPF on 2006-09-07 12:07:24 as along with 4 people bertelsen bobychan jfr aviad_work

Theme discovery from gene lists for identification and viewing of multiple functional groups.

BMC Bioinformatics, Vol. 6 (2005)

by P Pehkonen, G Wong, P Törönen

posted to algorithm functional_annotation gene_list_analysis by ealloza to the group BioinfoCIPF on 2006-08-24 12:43:38 as

Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data.

Bioinformatics, Vol. 20, No. 13. (1 September 2004), pp. 2156-2158.

by R Pandey, RK Guru, DW Mount

posted to expression functional_annotation gene_set_analysis microarray pathway visualisation by ealloza to the group BioinfoCIPF on 2006-08-23 14:47:23 as along with 2 people dragonrez tardigrade

Global functional profiling of gene expression.

Genomics, Vol. 81, No. 2. (February 2003), pp. 98-104.

by S Draghici, P Khatri, RP Martins, GC Ostermeier, SA Krawetz

posted to algorithm binomial expression functional_annotation microarray by ealloza to the group BioinfoCIPF on 2006-08-23 11:20:23 as along with 2 people tardigrade incovoma

Pathways to the analysis of microarray data

Trends in Biotechnology, Vol. 23, No. 8. (August 2005), pp. 429-435.

by Keira R Curtis, Matej Oresic, Antonio Vidal-Puig

posted to comparison expression functional_annotation gene_set_analysis microarray review by ealloza to the group BioinfoCIPF on 2006-08-22 19:21:44 as along with 5 people snuppepuppan textoris Ayest tardigrade heliopais

Group testing for pathway analysis improves comparability of different microarray data sets.

Bioinformatics (7 August 2006)

by Theodora Manoli, Norbert Gretz, Hermann-Josef J Gröne, Marc Kenzelmann, Roland Eils, Benedikt Brors

posted to comparison expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2006-08-22 15:19:45 as along with 4 people jfr jdiggans macavity1g ptrobajo

Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data.

Bioinformatics, Vol. 21, No. 9. (1 May 2005), pp. 1971-1978.

by C Lottaz, R Spang

posted to svd prediction ontology microarray functional_annotation expression classification algorithm by ealloza to the group BioinfoCIPF on 2006-08-21 16:57:17 as along with 1 person jfr

stam--a Bioconductor compliant R package for structured analysis of microarray data.

BMC Bioinformatics, Vol. 6 (2005)

by C Lottaz, R Spang

posted to svd prediction ontology microarray functional_annotation expression classification algorithm by ealloza to the group BioinfoCIPF on 2006-08-21 16:55:21 as along with 1 person jdiggans

Study of coordinative gene expression at the biological process level

Bioinformatics, Vol. 21, No. 18. (15 September 2005), pp. 3651-3657.

by Tianwei Yu, Wei Sun, Shinsheng Yuan, Ker-Chau Li

posted to systems_biology microarray functional_annotation expression coexpression algorithm by ealloza to the group BioinfoCIPF on 2006-08-21 13:49:30 as

Comparing functional annotation analyses with Catmap.

BMC Bioinformatics, Vol. 5, No. 1. (9 December 2004)

by T Breslin, P Edén, M Krogh

posted to algorithm expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2006-08-10 12:41:09 as along with 2 people and 2 groups raylim ana structural_bioinformatics Bioinformatics

ErmineJ: tool for functional analysis of gene expression data sets.

BMC Bioinformatics, Vol. 6 (2005)

by HK Lee, W Braynen, K Keshav, P Pavlidis

posted to expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2006-08-09 15:54:20 as along with 2 people raylim jdiggans

Exploring gene expression data with class scores.

Pac Symp Biocomput (2002), pp. 474-485.

by P Pavlidis, DP Lewis, WS Noble

posted to expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2006-08-09 12:36:32 as

T-profiler: scoring the activity of predefined groups of genes using gene expression data.

Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)

by A Boorsma, BC Foat, D Vis, F Klis, HJ Bussemaker

posted to expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2006-08-08 17:54:28 as along with 1 person jdiggans

Pathway level analysis of gene expression using singular value decomposition.

BMC Bioinformatics, Vol. 6 (2005)

by J Tomfohr, J Lu, TB Kepler

posted to algorithm expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2006-08-01 12:55:12 as along with 2 people fisherp waghsk

Expression profiling reveals fundamental biological differences in acute myeloid leukemia with isolated trisomy 8 and normal cytogenetics.

Proc Natl Acad Sci U S A, Vol. 98, No. 3. (30 January 2001), pp. 1124-1129.

by K Virtaneva, FA Wright, SM Tanner, B Yuan, WJ Lemon, MA Caligiuri, CD Bloomfield, A de La Chapelle , R Krahe

posted to algorithm expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2006-08-01 10:44:12 as along with 1 person bioguru2000

Significance analysis of functional categories in gene expression studies: a structured permutation approach

Bioinformatics, Vol. 21, No. 9. (1 May 2005), pp. 1943-1949.

by William T Barry, Andrew B Nobel, Fred A Wright

posted to algorithm expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2006-07-31 11:46:57 as along with 3 people jdiggans nedwards heliopais

Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles.

Bioinformatics, Vol. 22, No. 14. (July 2006), pp. e108-e116.

by E Edelman, A Porrello, J Guinney, B Balakumaran, A Bild, Pg Febbo, S Mukherjee

posted to algorithm expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2006-07-31 11:41:22 as along with 711 people and 130 groups 6rheology amydash dcastro boellernadja nafets sbaete steveut pathari alexispaz fghjorth tanneama000 MariaChiaraP ricckli iarmac laurabailey wolfe275 tkravitz pulsus-morbi Gaetan EsepBib jakobl ablam tbolt427 kungcc wartaalman austin Langster ezaydens Scis0000002 Axis jeanbean melody jsenn christiankissig psique scarcelan balicea danzinde gi0rgi0ne Stepstep abdulpur nlauzier mirweis christian_librarian skumagai nkishan squirmelia carterb Corbasson IanBrown malkav30 sarahmccrum gkvas freddan jago giolakat kndiaye gvandyk1 wongmld Neeperando duckysherwood yungyuc murb midshipman ranger vrich taenneken pdessus Repton nikko LTrottier mfloris hrwiltse scottkb ThomasKluge fernand0 dperkel egh jyuh samth sora florine ladygoat hopm hellige parmentierf ssn mortimer tinkha V plaugg ansobol mjaz berthelemy eldan pdlug zephoria carloscabanillas Janos bkliethermes nazareno elsantosneto januadiaboli yaroslavvb jurijmlotman geomblog srl bigga treycausey CSG mcphee chandrashekar denns matzke sherrivokey sona cassj lijil hlovise coolger incites bigmagpie alicetiara yorgos johannsen cavlec smbrower viller jenmy mlzafron tymmail sedging davidr macowell eimaj42jdp Flit BenWillems agallet hawesie sngourlay jolilius rmagf acer ville garyfeng danifazzio willwade gantlord melanieramage mgregg cwb neteler carneym crispinb rdlong lillekatt davemack agarza carsonr imcdnzl tjimenez Tolik lna dmikurube szityu michmill mamadoudiao kaniko applebyb joni2am P2324548 jpbenda Vaccine tadm mkwalker anar grzegorz japple planetoid okarsligil stormybriggs UWerplab nbr inbetweener pafmon stina pgastrein xiruela kutabar jfr xamde kliether mleis jshahin cmunson lfriedl sharonhoward ccots terraces czlamer brent_lance subhradeep jjray Jellyfish cmmorel bayesian benavides ghsalazar manuelpq sekulerlab jmaryott kristina chad_davis 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Automatic clustering of orthologs and inparalogs shared by multiple proteomes.

Bioinformatics, Vol. 22, No. 14. (15 July 2006)

by A Alexeyenko, I Tamas, G Liu, EL Sonnhammer

posted to functional_annotation orthology phylogeny by jhc to the group BioinfoCIPF on 2006-07-31 10:47:12 as along with 3 people and 1 group operon indigoviolet ninch EisenLab

Using the Gene Ontology for Microarray Data Mining: A Comparison of Methods and Application to Age Effects in Human Prefrontal Cortex

Neurochemical Research, Vol. 29, No. 6. (June 2004), pp. 1213-1222.

by Paul Pavlidis, Jie Qin, Victoria Arango, John J Mann, Etienne Sibille

posted to comparison expression functional_annotation microarray by ealloza to the group BioinfoCIPF on 2006-07-27 14:40:00 as along with 1 person dragonrez

Application of a priori established gene sets to discover biologically important differential expression in microarray data

PNAS, Vol. 102, No. 43. (25 October 2005), pp. 15278-15279.

by Andrea Bild, Phillip G Febbo

posted to expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2006-07-26 16:14:02 as along with 3 people srp33 maryee jdiggans

On methods for gene function scoring as a means of facilitating the interpretation of microarray results.

J Comput Biol, Vol. 13, No. 3. (April 2006), pp. 798-809.

by N Raghavan, D Amaratunga, J Cabrera, A Nie, J Qin, M