-
1
-
-
0038119396
-
Techniques of cluster algorithms in data mining
-
10.1023/A:1016308404627
-
Grabmeier J Rudolph A Techniques of cluster algorithms in data mining Data Min Knowl Disc 2002 6 303-360 10.1023/A:1016308404627
-
(2002)
Data Min Knowl Disc
, vol.6
, pp. 303-360
-
-
Grabmeier, J.1
Rudolph, A.2
-
4
-
-
1542399989
-
FatiGO: A web tool for finding significant associations of Gene Ontology terms with groups of genes
-
10.1093/bioinformatics/btg455 14990455
-
Al-Shahrour F Díaz-Uriarte R Dopazo J FatiGO: A web tool for finding significant associations of Gene Ontology terms with groups of genes Bioinformatics 2004 20 4 578-580 10.1093/bioinformatics/btg455 14990455
-
(2004)
Bioinformatics
, vol.20
, pp. 578-580
-
-
Al-Shahrour, F.1
Díaz-Uriarte, R.2
Dopazo, J.3
-
5
-
-
12344269924
-
GO::TermFinder - Open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
-
10.1093/bioinformatics/bth456 15297299
-
Boyle EI Weng S Gollub J Jin H Botstein D Cherry JM Sherlock G GO::TermFinder - open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes Bioinformatics 2004 20 3710-3715 10.1093/ bioinformatics/bth456 15297299
-
(2004)
Bioinformatics
, vol.20
, pp. 3710-3715
-
-
Boyle, E.I.1
Weng, S.2
Gollub, J.3
Jin, H.4
Botstein, D.5
Cherry, J.M.6
Sherlock, G.7
-
6
-
-
23044478689
-
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)
-
1190154 15998470 10.1186/1471-2105-6-168
-
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 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) BMC Bioinformatics 2005 6 168 1190154 15998470 10.1186/1471-2105-6-168
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 168
-
-
Zeeberg, B.R.1
Qin, H.2
Narasimhan, S.3
Sunshine, M.4
Cao, H.5
Kane, D.W.6
Reimers, M.7
Stephens, R.M.8
Bryant, D.9
Burt, S.K.10
Elnekave, E.11
Hari, D.M.12
Wynn, T.A.13
Cunningham-Rundles, C.14
Stewart, D.M.15
Nelson, D.16
Weinstein, J.N.17
-
7
-
-
0347513219
-
Characterizing gene sets with FuncAssociate
-
10.1093/bioinformatics/btg363 14668247
-
Berriz GF King OD Bryant B Sander C Roth FP Characterizing gene sets with FuncAssociate Bioinformatics 2003 19 2502-2504 10.1093/ bioinformatics/btg363 14668247
-
(2003)
Bioinformatics
, vol.19
, pp. 2502-2504
-
-
Berriz, G.F.1
King, O.D.2
Bryant, B.3
Sander, C.4
Roth, F.P.5
-
8
-
-
13244279520
-
Comparing functional annotation analysis with Catmap
-
543458 15588298 10.1186/1471-2105-5-193
-
Breslin T Edén P Krogh M Comparing functional annotation analysis with Catmap BMC Bioinformatics 2004 5 193 543458 15588298 10.1186/ 1471-2105-5-193
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 193
-
-
Breslin, T.1
Edén, P.2
Krogh, M.3
-
9
-
-
2942549112
-
A simple tool to enhance sensitivity and facilitate interpretation of microarray experiments
-
403636 15050037 10.1186/1471-2105-5-34
-
Breitling R Amtmann A Herzyk P Iterative Group Analysis (iGA) A simple tool to enhance sensitivity and facilitate interpretation of microarray experiments BMC Bioinformatics 2004 5 34 403636 15050037 10.1186/ 1471-2105-5-34
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 34
-
-
Breitling, R.1
Amtmann, A.2
Herzyk, P.3
-
10
-
-
21444442035
-
Discovery molecular functions significantly related to phenotypes by combining gene expression data and biological information
-
10.1093/bioinformatics/bti457 15840702
-
Al-Shahrour F Díaz-Uriarte R Dopazo J Discovery molecular functions significantly related to phenotypes by combining gene expression data and biological information Bioinformatics 2005 21 2988-2993 10.1093/bioinformatics/bti457 15840702
-
(2005)
Bioinformatics
, vol.21
, pp. 2988-2993
-
-
Al-Shahrour, F.1
Díaz-Uriarte, R.2
Dopazo, J.3
-
11
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
1239896 16199517 10.1073/pnas.0506580102
-
Subramanian A Tamayo P Mootha VK Mukherjee S Ebert BL Gillette MA Paulovich A Pomeroy SL Golub TR Lander ES Mesirov JP Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles Proc Natl Acad Sci USA 2005 102 15545-15550 1239896 16199517 10.1073/pnas.0506580102
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Gillette, M.A.6
Paulovich, A.7
Pomeroy, S.L.8
Golub, T.R.9
Lander, E.S.10
Mesirov, J.P.11
-
12
-
-
24644470505
-
Ontological analysis of gene expression data: Current tools, limitations, and open problems
-
10.1093/bioinformatics/bti565 15994189
-
Khatri P Dragici S Ontological analysis of gene expression data: Current tools, limitations, and open problems Bioinformatics 2005 21 3587-3595 10.1093/bioinformatics/bti565 15994189
-
(2005)
Bioinformatics
, vol.21
, pp. 3587-3595
-
-
Khatri, P.1
Dragici, S.2
-
13
-
-
33750946376
-
Functional interpretation of microarray experients
-
10.1089/omi.2006.10.398 17069516
-
Dopazo J Functional interpretation of microarray experients OMICS 2006 10 398-410 10.1089/omi.2006.10.398 17069516
-
(2006)
OMICS
, vol.10
, pp. 398-410
-
-
Dopazo, J.1
-
14
-
-
33847264343
-
Enrichment or depletion of a GO category within a class of genes: Which test?
-
10.1093/bioinformatics/btl633
-
Rivals I Personnaz L Taing L Potier MC Enrichment or depletion of a GO category within a class of genes: Which test? Bioinformatics 23 401 407 10.1093/bioinformatics/btl633 17182697
-
Bioinformatics
, vol.23
, pp. 401-407
-
-
Rivals, I.1
Personnaz, L.2
Taing, L.3
Potier, M.C.4
-
15
-
-
2942601249
-
Selection of informative clusters from hierarchical cluster tree with gene classes
-
407846 15043761 10.1186/1471-2105-5-32
-
Toronen P Selection of informative clusters from hierarchical cluster tree with gene classes BMC Bioinformatics 2004 5 32 407846 15043761 10.1186/1471-2105-5-32
-
(2004)
BMC Bioinformatics
, vol.5
, Issue.5
, pp. 32
-
-
Toronen, P.1
-
16
-
-
10244264786
-
The CRASSS plug-in for integrating annotation data with hierarchical clustering results
-
10.1093/bioinformatics/bth362 15201188
-
Buehler EC Sachs JR Shao K Bagchi A Ungar LH The CRASSS plug-in for integrating annotation data with hierarchical clustering results Bioinformatics 2004 20 3266-3269 10.1093/bioinformatics/bth362 15201188
-
(2004)
Bioinformatics
, vol.20
, pp. 3266-3269
-
-
Buehler, E.C.1
Sachs, J.R.2
Shao, K.3
Bagchi, A.4
Ungar, L.H.5
-
17
-
-
8844252982
-
THEA: Ontology-driven analysis of microarray data
-
10.1093/bioinformatics/bth295 15130932
-
Pasquier C Girardot F Jevardat de Fombelle K Christen R THEA: ontology-driven analysis of microarray data Bioinformatics 2004 20 2636-2643 10.1093/bioinformatics/bth295 15130932
-
(2004)
Bioinformatics
, vol.20
, pp. 2636-2643
-
-
Pasquier, C.1
Girardot, F.2
Jevardat de Fombelle, K.3
Christen, R.4
-
18
-
-
27744459345
-
A new algorithm for comparing and visualizing relationships between hierarchical and flat expression data clusterings
-
10.1093/bioinformatics/bti644 16141251
-
Torrente A Kapushesky M Brazma A A new algorithm for comparing and visualizing relationships between hierarchical and flat expression data clusterings Bioinformatics 2005 21 3993-3999 10.1093/bioinformatics/ bti644 16141251
-
(2005)
Bioinformatics
, vol.21
, pp. 3993-3999
-
-
Torrente, A.1
Kapushesky, M.2
Brazma, A.3
-
19
-
-
13844264514
-
Iterative cluster analysis of protein interaction data
-
10.1093/bioinformatics/bti021 15374873
-
Arnau V Mars S Marín I Iterative cluster analysis of protein interaction data Bioinformatics 2005 21 364-378 10.1093/bioinformatics/ bti021 15374873
-
(2005)
Bioinformatics
, vol.21
, pp. 364-378
-
-
Arnau, V.1
Mars, S.2
Marín, I.3
-
20
-
-
33644779012
-
Comparative genomics and protein domain graph analyses link ubiquitination and RNA metabolism
-
10.1016/j.jmb.2005.12.068 16426638
-
Lucas JI Arnau V Marín I Comparative genomics and protein domain graph analyses link ubiquitination and RNA metabolism J Mol Biol 2006 357 9-17 10.1016/j.jmb.2005.12.068 16426638
-
(2006)
J Mol Biol
, vol.357
, pp. 9-17
-
-
Lucas, J.I.1
Arnau, V.2
Marín, I.3
-
21
-
-
33748974481
-
UVPAR: Fast detection of functional shifts in duplicate genes
-
1570150 16569227 10.1186/1471-2105-7-174
-
Arnau V Gallach M Lucas JI Marín I UVPAR: Fast detection of functional shifts in duplicate genes BMC Bioinformatics 2006 7 174 1570150 16569227 10.1186/1471-2105-7-174
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 174
-
-
Arnau, V.1
Gallach, M.2
Lucas, J.I.3
Marín, I.4
-
22
-
-
84874666410
-
-
Web page containing a PERL script implementing the strategy developed in this article
-
Web page containing a PERL script implementing the strategy developed in this article http://www.uv.es/~genomica/treetracker
-
-
-
-
23
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
15070 15070 11102521
-
Gasch AP Spellman PT Kao CM Carmel-Harel O Eisen MB Storz G Botstein D Brown PO Genomic expression programs in the response of yeast cells to environmental changes Mol Biol Cell 11 4241-4257 15070 11102521
-
Mol Biol Cell
, vol.11
, pp. 4241-4257
-
-
Gasch, A.P.1
Spellman, P.T.2
Kao, C.M.3
Carmel-Harel, O.4
Eisen, M.B.5
Storz, G.6
Botstein, D.7
Brown, P.O.8
-
24
-
-
0036141992
-
Relating whole-genome expression data with protein-protein interactions
-
155252 11779829 10.1101/gr.205602
-
Jansen R Greenbaum D Gerstein M Relating whole-genome expression data with protein-protein interactions Genome Res 2002 12 37-46 155252 11779829 10.1101/gr.205602
-
(2002)
Genome Res
, vol.12
, pp. 37-46
-
-
Jansen, R.1
Greenbaum, D.2
Gerstein, M.3
-
25
-
-
0036279153
-
Protein interaction verification and functional annotation by integrated analysis of genome-scale data
-
10.1016/S1097-2765(02)00531-2 12049748
-
Kemmeren P van Berkum NL Vilo J Bijma T Donders R Brazma A Holstege FC Protein interaction verification and functional annotation by integrated analysis of genome-scale data Mol Cell 2002 9 1133-1143 10.1016/ S1097-2765(02)00531-2 12049748
-
(2002)
Mol Cell
, vol.9
, pp. 1133-1143
-
-
Kemmeren, P.1
van Berkum, N.L.2
Vilo, J.3
Bijma, T.4
Donders, R.5
Brazma, A.6
Holstege, F.C.7
-
26
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
24541 9843981 10.1073/pnas.95.25.14863
-
Eisen MB Spellman PT Brown PO Botstein D Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci USA 1998 95 14863-14868 24541 9843981 10.1073/pnas.95.25.14863
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 14863-14868
-
-
Eisen, M.B.1
Spellman, P.T.2
Brown, P.O.3
Botstein, D.4
-
27
-
-
0001457509
-
Some methods for classification and analysis of multivariate observation
-
MacQueen J Some methods for classification and analysis of multivariate observation Proc 5th Berk Symp 1967 1 281-297
-
(1967)
Proc 5th Berk Symp
, vol.1
, pp. 281-297
-
-
MacQueen, J.1
-
28
-
-
1842580761
-
Functional and topological characterization of protein interaction networks
-
10.1002/pmic.200300636 15048975
-
Yook SH Oltvai ZN Barabasi AL Functional and topological characterization of protein interaction networks Proteomics 2004 4 928-942 10.1002/pmic.200300636 15048975
-
(2004)
Proteomics
, vol.4
, pp. 928-942
-
-
Yook, S.H.1
Oltvai, Z.N.2
Barabasi, A.L.3
-
29
-
-
0035344460
-
Versatility of the mitochondrial protein import machinery
-
10.1038/35073006 11331908
-
Pfanner N Geissler A Versatility of the mitochondrial protein import machinery Nat Rev Mol Cell Biol 2001 2 339-349 10.1038/35073006 11331908
-
(2001)
Nat Rev Mol Cell Biol
, vol.2
, pp. 339-349
-
-
Pfanner, N.1
Geissler, A.2
-
30
-
-
4344640696
-
The mitochondrial morphology protein Mdm10 functions in assembly of the preprotein translocase of the outer membrane
-
10.1016/j.devcel.2004.06.003 15239954
-
Meisinger C Rissler M Chacinska A Szklarz LK Milenkovic D Kozjak V Schonfisch B Lohaus C Meyer HE Yaffe MP Guiard B Wiedemann N Pfanner N The mitochondrial morphology protein Mdm10 functions in assembly of the preprotein translocase of the outer membrane Dev Cell 2004 7 61-71 10.1016/j.devcel.2004.06.003 15239954
-
(2004)
Dev Cell
, vol.7
, pp. 61-71
-
-
Meisinger, C.1
Rissler, M.2
Chacinska, A.3
Szklarz, L.K.4
Milenkovic, D.5
Kozjak, V.6
Schonfisch, B.7
Lohaus, C.8
Meyer, H.E.9
Yaffe, M.P.10
Guiard, B.11
Wiedemann, N.12
Pfanner, N.13
-
31
-
-
20244373481
-
Mitochondrial presequence translocase: Switching between TOM tethering and motor recruitment involves Tim21 and Tim17
-
10.1016/j.cell.2005.01.011 15797382
-
Chacinska A Lind M Frazier AE Dudek J Meisinger C Geissler A Sickmann A Meyer HE Truscott KN Guiard B Pfanner N Rehling P Mitochondrial presequence translocase: Switching between TOM tethering and motor recruitment involves Tim21 and Tim17 Cell 2005 120 817-829 10.1016/ j.cell.2005.01.011 15797382
-
(2005)
Cell
, vol.120
, pp. 817-829
-
-
Chacinska, A.1
Lind, M.2
Frazier, A.E.3
Dudek, J.4
Meisinger, C.5
Geissler, A.6
Sickmann, A.7
Meyer, H.E.8
Truscott, K.N.9
Guiard, B.10
Pfanner, N.11
Rehling, P.12
-
32
-
-
0344442851
-
Identification and functional reconstitution of yeast mitochondrial carrier for S-adenosylmethionine
-
275433 14609944 10.1093/emboj/cdg574
-
Marobbio CM Agrimi G Larorsa FM Palmieri F Identification and functional reconstitution of yeast mitochondrial carrier for S-adenosylmethionine EMBO J 2003 22 5975-5982 275433 14609944 10.1093/emboj/cdg574
-
(2003)
EMBO J
, vol.22
, pp. 5975-5982
-
-
Marobbio, C.M.1
Agrimi, G.2
Larorsa, F.M.3
Palmieri, F.4
-
33
-
-
33644912080
-
Proteomic analysis of the yeast mitochondrial outer membrane reveals accumulation of a subclass of preproteins
-
1382330 16407407 10.1091/mbc.E05-08-0740
-
Zahedi RP Sickmann A Boehm AM Winkler C Zufall N Schonfisch B Guiard B Pfanner N Meisinger C Proteomic analysis of the yeast mitochondrial outer membrane reveals accumulation of a subclass of preproteins Mol Biol Cell 2006 17 1436-1450 1382330 16407407 10.1091/mbc.E05-08-0740
-
(2006)
Mol Biol Cell
, vol.17
, pp. 1436-1450
-
-
Zahedi, R.P.1
Sickmann, A.2
Boehm, A.M.3
Winkler, C.4
Zufall, N.5
Schonfisch, B.6
Guiard, B.7
Pfanner, N.8
Meisinger, C.9
-
34
-
-
0035902526
-
Biosynthesis of the thiazole moiety of thiamin in Escherichia coli: Identification of an acyldisulfide-linked protein - Protein conjugate that is functionally analogous to the ubiquitin/E1 complex
-
37467 11438688 10.1073/pnas.141226698
-
Xi J Ge Y Kinsland C McLafferty FW Begley TP Biosynthesis of the thiazole moiety of thiamin in Escherichia coli: Identification of an acyldisulfide-linked protein - protein conjugate that is functionally analogous to the ubiquitin/E1 complex Proc Natl Acad Sci USA 2001 98 8513-8518 37467 11438688 10.1073/pnas.141226698
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 8513-8518
-
-
Xi, J.1
Ge, Y.2
Kinsland, C.3
McLafferty, F.W.4
Begley, T.P.5
-
35
-
-
49549122021
-
Saccharomyces Genome Database
-
Saccharomyces Genome Database http://www.yeastgenome.org
-
-
-
-
36
-
-
84886763584
-
MeV 4.0
-
MeV 4.0 http://www.tm4.org
-
-
-
-
37
-
-
0037311919
-
TM4: A free, open-source system for microarray data management and analysis
-
12613259
-
Saeed AI Sharov V White J Li J Liang W Bhagabati N Braisted J Klapa M Currier T Thiagarajan M Sturn A Snuffin M Rezantsev A Popov D Ryltsov A Kostukovich E Borisovsky I Liu Z Vinsavich A Trush V Quackenbush J TM4: a free, open-source system for microarray data management and analysis Biotechniques 2003 34 374-378 12613259
-
(2003)
Biotechniques
, vol.34
, pp. 374-378
-
-
Saeed, A.I.1
Sharov, V.2
White, J.3
Li, J.4
Liang, W.5
Bhagabati, N.6
Braisted, J.7
Klapa, M.8
Currier, T.9
Thiagarajan, M.10
Sturn, A.11
Snuffin, M.12
Rezantsev, A.13
Popov, D.14
Ryltsov, A.15
Kostukovich, E.16
Borisovsky, I.17
Liu, Z.18
Vinsavich, A.19
Trush, V.20
Quackenbush, J.21
more..
-
38
-
-
0034616930
-
Functional discovery via a compendium of expression profiles
-
10.1016/S0092-8674(00)00015-5 10929718
-
Hughes TR Marton MJ Jones AR Roberts CJ Stoughton R Armour CD Bennett HA Coffey E Dai H He YD Kidd MJ King AM Meyer MR Slade D Lum PY Stepaniants SB Shoemaker DD Gachotte D Chakraburtty K Simon J Bard M Friend SH Functional discovery via a compendium of expression profiles Cell 2000 102 109-126 10.1016/S0092-8674(00)00015-5 10929718
-
(2000)
Cell
, vol.102
, pp. 109-126
-
-
Hughes, T.R.1
Marton, M.J.2
Jones, A.R.3
Roberts, C.J.4
Stoughton, R.5
Armour, C.D.6
Bennett, H.A.7
Coffey, E.8
Dai, H.9
He, Y.D.10
Kidd, M.J.11
King, A.M.12
Meyer, M.R.13
Slade, D.14
Lum, P.Y.15
Stepaniants, S.B.16
Shoemaker, D.D.17
Gachotte, D.18
Chakraburtty, K.19
Simon, J.20
Bard, M.21
Friend, S.H.22
more..
-
39
-
-
84886765577
-
Public microarray expression data at Michael Eisen laboratory
-
Public microarray expression data at Michael Eisen laboratory http://rana.lbl.gov/data/yeast/yeastall_public.txt.gz
-
-
-
|