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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:21, 17 September 2013


Full id: C370_acute_chronic_leukemia_CD34_testicular_Mast_H9



Phase1 CAGE Peaks

Hg19::chr11:75063275..75063314,-p6@ARRB1
Hg19::chr12:42836335..42836348,+p6@PPHLN1
Hg19::chr12:62654594..62654600,-p@chr12:62654594..62654600
-
Hg19::chr13:109248512..109248524,+p5@MYO16
Hg19::chr13:75900665..75900679,-p17@TBC1D4
Hg19::chr13:76056524..76056549,-p7@TBC1D4
Hg19::chr13:95713920..95713924,-p@chr13:95713920..95713924
-
Hg19::chr14:93460574..93460583,-p@chr14:93460574..93460583
-
Hg19::chr16:20837868..20837883,+p@chr16:20837868..20837883
+
Hg19::chr16:81685852..81685866,+p@chr16:81685852..81685866
+
Hg19::chr16:89043267..89043276,-p13@CBFA2T3
Hg19::chr17:80159702..80159743,-p1@CU691842
Hg19::chr18:9191997..9192008,+p@chr18:9191997..9192008
+
Hg19::chr1:110922677..110922681,-p@chr1:110922677..110922681
-
Hg19::chr1:35309235..35309266,-p@chr1:35309235..35309266
-
Hg19::chr2:190448678..190448702,-p5@SLC40A1
Hg19::chr3:77248792..77248797,+p@chr3:77248792..77248797
+
Hg19::chr4:83763487..83763502,-p16@SEC31A
Hg19::chr6:136687008..136687031,-p@chr6:136687008..136687031
-
Hg19::chr8:129057463..129057484,+p@chr8:129057463..129057484
+
Hg19::chr8:129057486..129057490,+p@chr8:129057486..129057490
+
Hg19::chr8:129057497..129057520,+p@chr8:129057497..129057520
+
Hg19::chr8:129057554..129057590,+p@chr8:129057554..129057590
+
Hg19::chr8:129057598..129057610,+p@chr8:129057598..129057610
+
Hg19::chr8:129057633..129057641,+p@chr8:129057633..129057641
+
Hg19::chr8:130393776..130393785,-p@chr8:130393776..130393785
-
Hg19::chr9:14214432..14214451,-p@chr9:14214432..14214451
-
Hg19::chr9:21975236..21975249,-p15@CDKN2A
Hg19::chrX:109564494..109564506,-p@chrX:109564494..109564506
-
Hg19::chrX:49005043..49005049,-p@chrX:49005043..49005049
-


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0005737cytoplasm0.0188488682984112
GO:0051329interphase of mitotic cell cycle0.0188488682984112
GO:0051325interphase0.0188488682984112
GO:0032502developmental process0.0227530865416551
GO:0010149senescence0.0227530865416551
GO:0030135coated vesicle0.0227530865416551
GO:0008283cell proliferation0.0227530865416551
GO:0048856anatomical structure development0.0256749525653224
GO:0032088inhibition of NF-kappaB transcription factor0.0265025818339062
GO:0008285negative regulation of cell proliferation0.0265025818339062
GO:0045786negative regulation of progression through cell cycle0.0265025818339062
GO:0005622intracellular0.0265025818339062
GO:0005381iron ion transmembrane transporter activity0.0265025818339062
GO:0009653anatomical structure morphogenesis0.0265025818339062
GO:0001953negative regulation of cell-matrix adhesion0.0265025818339062
GO:0045749negative regulation of S phase of mitotic cell cycle0.0265025818339062
GO:0022037metencephalon development0.0265025818339062
GO:0021549cerebellum development0.0265025818339062
GO:0045736negative regulation of cyclin-dependent protein kinase activity0.0265025818339062
GO:0022408negative regulation of cell-cell adhesion0.0265025818339062
GO:0000278mitotic cell cycle0.0265025818339062
GO:0007090regulation of S phase of mitotic cell cycle0.0265025818339062
GO:0016023cytoplasmic membrane-bound vesicle0.0265025818339062
GO:0042326negative regulation of phosphorylation0.0265025818339062
GO:0031988membrane-bound vesicle0.0265025818339062
GO:0000074regulation of progression through cell cycle0.0265025818339062
GO:0051726regulation of cell cycle0.0265025818339062
GO:0012507ER to Golgi transport vesicle membrane0.0265025818339062
GO:0030127COPII vesicle coat0.0265025818339062
GO:0045930negative regulation of progression through mitotic cell cycle0.0265025818339062
GO:0022407regulation of cell-cell adhesion0.0265025818339062
GO:0001952regulation of cell-matrix adhesion0.0265025818339062
GO:0045936negative regulation of phosphate metabolic process0.0265025818339062
GO:0000139Golgi membrane0.0265025818339062
GO:0022403cell cycle phase0.0265025818339062
GO:0030134ER to Golgi transport vesicle0.0272896184018127
GO:0033261regulation of progression through S phase0.0272896184018127
GO:0004861cyclin-dependent protein kinase inhibitor activity0.0272896184018127
GO:0004857enzyme inhibitor activity0.0276506314564587
GO:0043433negative regulation of transcription factor activity0.0276506314564587
GO:0000084S phase of mitotic cell cycle0.0280542987215237
GO:0044431Golgi apparatus part0.0280542987215237
GO:0031410cytoplasmic vesicle0.0280542987215237
GO:0051059NF-kappaB binding0.0280542987215237
GO:0031982vesicle0.0280542987215237
GO:0051320S phase0.03125657187156
GO:0042127regulation of cell proliferation0.03125657187156
GO:0043231intracellular membrane-bound organelle0.03125657187156
GO:0043227membrane-bound organelle0.03125657187156
GO:0030902hindbrain development0.0317753063555054
GO:0007162negative regulation of cell adhesion0.0345277058246334
GO:0007568aging0.0345277058246334
GO:0044424intracellular part0.0347018085760933
GO:0048869cellular developmental process0.0369192915608153
GO:0030154cell differentiation0.0369192915608153
GO:0046915transition metal ion transmembrane transporter activity0.0369787330250068
GO:0030658transport vesicle membrane0.0374306449734218
GO:0030660Golgi-associated vesicle membrane0.0374306449734218
GO:0007346regulation of progression through mitotic cell cycle0.0374306449734218
GO:0000082G1/S transition of mitotic cell cycle0.039099171745683
GO:0050790regulation of catalytic activity0.0397954447486252
GO:0005834heterotrimeric G-protein complex0.0409510098350862
GO:0022402cell cycle process0.0409510098350862
GO:0031424keratinization0.0409510098350862
GO:0051015actin filament binding0.0411677125813885
GO:0006888ER to Golgi vesicle-mediated transport0.0411677125813885
GO:0004860protein kinase inhibitor activity0.0411677125813885
GO:0019210kinase inhibitor activity0.0423330587829715
GO:0065007biological regulation0.0423330587829715
GO:0065009regulation of a molecular function0.0423330587829715
GO:0005794Golgi apparatus0.0446511865436426
GO:0009913epidermal cell differentiation0.045099006639002
GO:0000079regulation of cyclin-dependent protein kinase activity0.045099006639002
GO:0019897extrinsic to plasma membrane0.045099006639002
GO:0030120vesicle coat0.045099006639002
GO:0030662coated vesicle membrane0.045099006639002
GO:0051090regulation of transcription factor activity0.045099006639002
GO:0030308negative regulation of cell growth0.045099006639002
GO:0015082di-, tri-valent inorganic cation transmembrane transporter activity0.045099006639002
GO:0045792negative regulation of cell size0.045099006639002
GO:0048730epidermis morphogenesis0.045099006639002
GO:0006879cellular iron ion homeostasis0.045099006639002
GO:0000075cell cycle checkpoint0.045099006639002
GO:0055072iron ion homeostasis0.045099006639002
GO:0006826iron ion transport0.045099006639002
GO:0006469negative regulation of protein kinase activity0.045099006639002
GO:0033673negative regulation of kinase activity0.045099006639002
GO:0051348negative regulation of transferase activity0.0461414558060958
GO:0045926negative regulation of growth0.0467159056500954
GO:0030133transport vesicle0.0467159056500954
GO:0044444cytoplasmic part0.0467159056500954
GO:0042325regulation of phosphorylation0.0467159056500954
GO:0048471perinuclear region of cytoplasm0.0467159056500954
GO:0043229intracellular organelle0.0467159056500954
GO:0043226organelle0.0467159056500954
GO:0030155regulation of cell adhesion0.0468357472001047
GO:0007049cell cycle0.0468357472001047
GO:0051174regulation of phosphorus metabolic process0.0474377394209792
GO:0019220regulation of phosphate metabolic process0.0474377394209792
GO:0005798Golgi-associated vesicle0.0474377394209792
GO:0048729tissue morphogenesis0.048995016963446
GO:0008021synaptic vesicle0.0498520403523731



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br><br>disease_data<br>

Disease
Ontology termp-valuen
chronic leukemia2.97e-688
myeloid leukemia2.06e-4831
leukemia2.40e-3839
hematologic cancer3.74e-2951
immune system cancer3.74e-2951
chronic myeloid leukemia5.53e-171
organ system cancer3.28e-10137


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.000411655
MA0004.10.31844
MA0006.10.0332857
MA0007.10.0871398
MA0009.10.417521
MA0014.10.000158399
MA0017.10.173605
MA0019.10.180682
MA0024.10.332558
MA0025.10.531977
MA0027.11.95983
MA0028.10.149896
MA0029.10.347825
MA0030.10.338746
MA0031.10.288912
MA0038.10.15256
MA0040.10.352485
MA0041.10.699566
MA0042.11.04524
MA0043.10.417784
MA0046.11.85353
MA0048.10.246211
MA0050.11.04825
MA0051.10.457885
MA0052.10.355576
MA0055.10.152031
MA0056.10
MA0057.10.0611057
MA0058.10.443744
MA0059.10.0541371
MA0060.10.0090143
MA0061.10.0954482
MA0063.10
MA0066.10.152817
MA0067.10.697961
MA0068.10.134205
MA0069.11.04516
MA0070.11.02498
MA0071.10.407159
MA0072.11.01688
MA0073.10.0300383
MA0074.10.149576
MA0076.10.060743
MA0077.13.64993
MA0078.10.612611
MA0081.10.441387
MA0083.11.08548
MA0084.10.873335
MA0087.10.390315
MA0088.10.258233
MA0089.10
MA0090.10.236197
MA0091.10.0974512
MA0092.10.574995
MA0093.10.585007
MA0095.10
MA0098.10
MA0100.10.161006
MA0101.10.0351297
MA0103.10.298707
MA0105.10.0176079
MA0106.11.01152
MA0107.10.0171106
MA0108.20.286605
MA0109.10
MA0111.10.538416
MA0113.10.188804
MA0114.10.191937
MA0115.10.62811
MA0116.10.20531
MA0117.10.449155
MA0119.10.0483167
MA0122.10.471243
MA0124.10.590699
MA0125.10.516292
MA0130.10
MA0131.10.226279
MA0132.10
MA0133.10
MA0135.10.443024
MA0136.10.474844
MA0139.10.18088
MA0140.14.05306
MA0141.10.197657
MA0142.10.265252
MA0143.10.188919
MA0144.11.19581
MA0145.10.0247161
MA0146.10.0286167
MA0147.10.0831159
MA0148.10.1088
MA0149.13.20749
MA0062.20.0896156
MA0035.21.88896
MA0039.20.00392183
MA0138.20.214585
MA0002.20.0397706
MA0137.20.358888
MA0104.20.0455118
MA0047.20.508505
MA0112.20.772023
MA0065.20.206209
MA0150.10.853276
MA0151.10
MA0152.10.819035
MA0153.11.25287
MA0154.10.0166134
MA0155.10.00122211
MA0156.10.0408263
MA0157.10.245386
MA0158.10
MA0159.10.018627
MA0160.10.116872
MA0161.10
MA0162.10.00257347
MA0163.10.00607708
MA0164.10.196993
MA0080.20.137324
MA0018.20.179075
MA0099.20.413335
MA0079.25.15207e-07
MA0102.20.908736
MA0258.10.156771
MA0259.10.0202561
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#905122.534480630785050.001249154263782790.00839837917826773
ELF1#1997131.845175782149930.01287805852090080.0463256140896345
EP300#2033112.483778632948510.002584063500042490.0142935759695428
GATA1#2623188.136184886280261.49657903612219e-132.29854732284655e-11
GATA2#2624156.3724658667771.29303195975262e-091.17021633314215e-07
HDAC2#3066114.919060753429635.6421765724406e-060.000170110646376768
HMGN3#932492.453564317005180.007829905321452980.0321580668475845
JUN#372583.336754451289690.001958835897867990.0115041816531201
JUNB#372677.142480953958274.15293116006154e-050.000752869254340683
REST#5978103.216676238709340.0006034595302459170.00503955780260301
STAT1#677264.141317499439840.002759470920623080.01512841908026
STAT2#6773817.40367231638421.30418599998989e-089.62599870338831e-07
TAL1#68861615.92992889463482.2751293851679e-164.47480673931357e-14



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C370&oldid=3067487"