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Tag functional_annotation [56 articles]

Recent papers classified by the tag functional_annotation.
  • notes Functional genome annotation through phylogenomic mapping
    Nature Biotechnology, Vol. 23, No. 6. (06 June 2005), pp. 691-698.
    by Balaji S Srinivasan, Nora B Caberoy, Garret Suen, Rion G Taylor, Radhika Shah, Farah Tengra, Barry S Goldman, Anthony G Garza, Roy D Welch
    posted to functional_annotation phylogenetics by setar on 2005-06-20 16:00:44 as read along with 11 people and 1 group shoshin operon tmmurali pggm aprasad balajis nuke2005 lyongu nedwards blobbybirdman kroos Myxo group
  • 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 on 2006-07-31 10:47:12 as **** along with 3 people and 2 groups operon indigoviolet ninch EisenLab BioinfoCIPF
  • Functional classification using phylogenomic inference.
    PLoS Comput Biol, Vol. 2, No. 6. (30 June 2006)
    by D Brown, K Sjölander
    posted to functional_annotation phylogeny by jhc on 2006-07-26 10:02:06 as read along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • Multievidence microarray mining.
    Trends Genet, Vol. 21, No. 10. (October 2005), pp. 553-558.
    by M Seifert, M Scherf, A Epple, T Werner
    posted to functional_annotation microarray by heliopais on 2008-02-22 13:59:50 as ***** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • JASPAR: an open-access database for eukaryotic transcription factor binding profiles.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by A Sandelin, W Alkema, P Engström, WW Wasserman, B Lenhard
    posted to database functional_annotation transcription_factor by heliopais on 2008-02-22 13:39:03 as ** along with 4 people and 2 groups aalibes indigoviolet jguinney nklee EisenLab Motif Discovery
  • 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 read 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
  • 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 read 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 read 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 read along with 1 person jdiggans
  • 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 read 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 read
  • 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 read 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 read 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 read along with 1 person bioguru2000
  • 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 read 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 read 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 McMillian
    posted to comparison expression functional_annotation microarray by ealloza to the group BioinfoCIPF on 2006-07-25 16:22:31 as read along with 1 person jdiggans
  • PAGE: parametric analysis of gene set enrichment.
    BMC Bioinformatics, Vol. 6 (2005)
    by SY Kim, DJ Volsky
    posted to algorithm expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2006-07-24 17:20:44 as read along with 5 people giovenko heliopais srp33 jdiggans waghsk
  • 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
  • PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes.
    Nat Genet, Vol. 34, No. 3. (July 2003), pp. 267-273.
    by VK Mootha, CM Lindgren, KF Eriksson, A Subramanian, S Sihag, J Lehar, P Puigserver, E Carlsson, M Ridderstråle, E Laurila, N Houstis, MJ Daly, N Patterson, JP Mesirov, TR Golub, P Tamayo, B Spiegelman, ES Lander, JN Hirschhorn, D Altshuler, LC Groop
    posted to algorithm expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2006-07-20 15:51:52 as read along with 6 people and 1 group heliopais magusina dragonrez maryee giovanni shikin GeschwindLab
  • 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 read along with 7 people giovenko heliopais srp33 dragonrez maryee frohike justescaped
  • 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 read along with 3 people jyuh rdiaz mayercd
  • From the Cover: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    PNAS, Vol. 102, No. 43. (25 October 2005), pp. 15545-15550.
    by Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander, Jill P Mesirov
    posted to algorithm expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2006-07-20 15:41:43 as read along with 22 people and 3 groups AbnerCYH sgoetz ellakat ihpark srp33 dragonrez jfr balajis maryee xwbcn hpiwowar aviad_work jdiggans jeremymiller frohike hawkeyehammer schuylrp natstreet heliopais shikin waghsk roys Bioinformatics GeschwindLab Indigene
  • 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 *****
  • 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 read along with 2 people and 2 groups raylim ana structural_bioinformatics Bioinformatics
  • 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 read along with 1 person macavity1g
  • 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 ***
  • 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 read 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 read along with 6 people and 1 group ndiaz giovanni jdiggans uprock heliopais waghsk GeschwindLab
  • 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 read
  • 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 read along with 5 people snuppepuppan textoris Ayest tardigrade heliopais
  • 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 read along with 3 people jdiggans nedwards heliopais
  • 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 read along with 2 people jdiggans heliopais
  • 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
  • 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
  • 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
  • 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 read
  • 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 read
  • 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 read
  • 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 read 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 read along with 5 people and 1 group diging_data jyuh heliopais jfr shigepong BTS-PT-AS-CS
  • 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 read along with 2 people and 1 group shigepong MrBrownShoes NBI
  • 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
  • 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 read along with 6 people srp33 jyuh jfr emb51 Garamonfok cerami
  • Systematic functional characterization of cis-regulatory motifs in human core promoters
    Genome Res. (6 February 2008), gr.6828808.
    by Saurabh Sinha, Adam S Adler, Yair Field, Howard Y Chang, Eran Segal
    posted to functional_annotation genome-wide human microrna post-transcriptional regulation transcription transcription_factor by ealloza on 2008-03-03 10:17:18 as *** along with 7 people and 1 group isimpson ihpark gracio lp2 cabbagezs idonaldson emptyhb Jarman Lab
  • notes miRGator: an integrated system for functional annotation of microRNAs.
    Nucleic Acids Res (16 October 2007)
    by Seungyoon Nam, Bumjin Kim, Seokmin Shin, Sanghyuk Lee
    posted to coexpression correlation database expression functional_annotation gene_set_analysis microrna webserver by ealloza on 2007-11-12 12:51:36 as read along with 2 people jfr maralena
  • Computational analysis of biological functions and pathways collectively targeted by co-expressed microRNAs in cancer
    BMC Bioinformatics, Vol. 8, No. Suppl 7. (2007)
    by Yuriy Gusev, Thomas Schmittgen, Megan Lerner, Russell Postier, Daniel Brackett
    posted to cancer coexpression functional_annotation microrna pathway by ealloza on 2007-12-13 17:58:22 as read along with 5 people jfr eckart_bindewald vinithepooh yugusev maralena
  • The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease.
    Science, Vol. 313, No. 5795. (29 September 2006), pp. 1929-1935.
    by J Lamb, ED Crawford, D Peck, JW Modell, IC Blat, MJ Wrobel, J Lerner, JP Brunet, A Subramanian, KN Ross, M Reich, H Hieronymus, G Wei, SA Armstrong, SJ Haggarty, PA Clemons, R Wei, SA Carr, ES Lander, TR Golub
    posted to connectivity expression functional_annotation map signature by ealloza on 2006-10-04 17:48:54 as read along with 21 people and 9 groups askrajiv BragilMassoud jyuh kuhn jfr yas balajis marcius lhonigberg neveaire kengg koller mlovell jdiggans ezra jeremymiller frohike massivemayhem lp2 pablomendes jdiezperezj Biostatistics Computational-Genomics Bioinformatics Neuroscience T_lab BioinfoCIPF SGU-CIPF GeschwindLab Plantandetc
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