Personal tools

Coexpression cluster:C169: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
Line 1: Line 1:
{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 10:47, 17 September 2013


Full id: C169_hereditary_adult_gall_lymphangiectasia_chronic_b_choriocarcinoma



Phase1 CAGE Peaks

Hg19::chr10:129780311..129780325,+p@chr10:129780311..129780325
+
Hg19::chr11:12017002..12017006,-p@chr11:12017002..12017006
-
Hg19::chr11:45077600..45077605,-p@chr11:45077600..45077605
-
Hg19::chr12:101114061..101114068,+p@chr12:101114061..101114068
+
Hg19::chr12:111115637..111115643,-p@chr12:111115637..111115643
-
Hg19::chr12:129886232..129886236,+p@chr12:129886232..129886236
+
Hg19::chr12:54430774..54430776,+p@chr12:54430774..54430776
+
Hg19::chr12:54430838..54430849,+p@chr12:54430838..54430849
+
Hg19::chr12:54430878..54430894,+p@chr12:54430878..54430894
+
Hg19::chr13:36788658..36788703,-p2@CCDC169-SOHLH2
p2@SOHLH2
Hg19::chr13:36788718..36788729,-p3@CCDC169-SOHLH2
p3@SOHLH2
Hg19::chr13:90031692..90031701,-p@chr13:90031692..90031701
-
Hg19::chr13:90054694..90054707,+p@chr13:90054694..90054707
+
Hg19::chr13:98832731..98832745,+p@chr13:98832731..98832745
+
Hg19::chr14:100485632..100485641,-p@chr14:100485632..100485641
-
Hg19::chr14:100485707..100485728,-p@chr14:100485707..100485728
-
Hg19::chr14:100485712..100485727,+p14@EVL
Hg19::chr14:100485738..100485745,+p37@EVL
Hg19::chr14:106347250..106347263,-p@chr14:106347250..106347263
-
Hg19::chr14:106453005..106453010,-p1@HM995871
Hg19::chr14:25495787..25495796,-p@chr14:25495787..25495796
-
Hg19::chr14:72944734..72944763,+p@chr14:72944734..72944763
+
Hg19::chr14:93336950..93336968,-p@chr14:93336950..93336968
-
Hg19::chr15:23841916..23841926,-p@chr15:23841916..23841926
-
Hg19::chr15:52404898..52404917,-p4@BCL2L10
Hg19::chr15:52404921..52404940,-p2@BCL2L10
Hg19::chr15:83368645..83368652,-p@chr15:83368645..83368652
-
Hg19::chr15:96537325..96537333,-p@chr15:96537325..96537333
-
Hg19::chr15:96539848..96539851,-p@chr15:96539848..96539851
-
Hg19::chr15:99539699..99539703,+p@chr15:99539699..99539703
+
Hg19::chr16:55880765..55880779,-p@chr16:55880765..55880779
-
Hg19::chr17:11711799..11711827,-p@chr17:11711799..11711827
-
Hg19::chr17:21251902..21251907,-p@chr17:21251902..21251907
-
Hg19::chr17:34206860..34206865,-p@chr17:34206860..34206865
-
Hg19::chr17:51127122..51127127,-p@chr17:51127122..51127127
-
Hg19::chr17:51147371..51147377,+p@chr17:51147371..51147377
+
Hg19::chr17:59322535..59322541,-p@chr17:59322535..59322541
-
Hg19::chr17:59322564..59322600,+p5@BCAS3
Hg19::chr17:60536002..60536040,+p4@TLK2
Hg19::chr17:70016724..70016733,-p@chr17:70016724..70016733
-
Hg19::chr18:56320706..56320709,+p@chr18:56320706..56320709
+
Hg19::chr18:59518131..59518142,-p@chr18:59518131..59518142
-
Hg19::chr18:59518164..59518170,-p@chr18:59518164..59518170
-
Hg19::chr18:60662408..60662414,+p@chr18:60662408..60662414
+
Hg19::chr19:28913175..28913210,+p@chr19:28913175..28913210
+
Hg19::chr1:15482761..15482763,-p@chr1:15482761..15482763
-
Hg19::chr1:15563005..15563040,+p@chr1:15563005..15563040
+
Hg19::chr1:15563067..15563079,+p@chr1:15563067..15563079
+
Hg19::chr1:159267075..159267096,+p@chr1:159267075..159267096
+
Hg19::chr1:210573062..210573064,-p@chr1:210573062..210573064
-
Hg19::chr1:229504069..229504072,-p@chr1:229504069..229504072
-
Hg19::chr1:24581338..24581346,-p1@uc001biw.2
Hg19::chr1:24581364..24581374,-p@chr1:24581364..24581374
-
Hg19::chr1:25876348..25876361,+p5@LDLRAP1
Hg19::chr1:25876368..25876381,+p6@LDLRAP1
Hg19::chr1:25876405..25876417,+p8@LDLRAP1
Hg19::chr20:25475219..25475229,-p@chr20:25475219..25475229
-
Hg19::chr20:56058118..56058120,-p@chr20:56058118..56058120
-
Hg19::chr20:56058449..56058484,+p@chr20:56058449..56058484
+
Hg19::chr20:59009589..59009592,+p@chr20:59009589..59009592
+
Hg19::chr22:25075039..25075064,+p@chr22:25075039..25075064
+
Hg19::chr22:25075096..25075120,+p@chr22:25075096..25075120
+
Hg19::chr22:33206569..33206577,+p@chr22:33206569..33206577
+
Hg19::chr22:33206603..33206608,+p@chr22:33206603..33206608
+
Hg19::chr22:33206615..33206622,+p@chr22:33206615..33206622
+
Hg19::chr22:33221188..33221202,+p@chr22:33221188..33221202
+
Hg19::chr22:47883693..47883699,-p@chr22:47883693..47883699
-
Hg19::chr2:135361356..135361362,-p@chr2:135361356..135361362
-
Hg19::chr2:173750319..173750340,-p@chr2:173750319..173750340
-
Hg19::chr2:206489395..206489396,-p@chr2:206489395..206489396
-
Hg19::chr2:45490454..45490486,-p@chr2:45490454..45490486
-
Hg19::chr3:106921810..106921817,-p@chr3:106921810..106921817
-
Hg19::chr3:106921835..106921857,-p@chr3:106921835..106921857
-
Hg19::chr3:128579995..128580003,+p@chr3:128579995..128580003
+
Hg19::chr3:133185639..133185654,+p@chr3:133185639..133185654
+
Hg19::chr3:184113225..184113231,-p@chr3:184113225..184113231
-
Hg19::chr3:25449881..25449891,-p@chr3:25449881..25449891
-
Hg19::chr4:170719812..170719813,+p@chr4:170719812..170719813
+
Hg19::chr5:132587921..132587932,-p5@FSTL4
Hg19::chr5:132587961..132587985,-p3@FSTL4
Hg19::chr6:144724237..144724255,+p@chr6:144724237..144724255
+
Hg19::chr6:32582541..32582590,-p@chr6:32582541..32582590
-
Hg19::chr7:140980284..140980289,+p@chr7:140980284..140980289
+
Hg19::chr7:22136603..22136614,+p@chr7:22136603..22136614
+
Hg19::chr7:69393144..69393149,-p@chr7:69393144..69393149
-
Hg19::chr7:69393274..69393286,+p@chr7:69393274..69393286
+
Hg19::chr7:70419611..70419618,+p@chr7:70419611..70419618
+
Hg19::chr8:105291143..105291166,-p@chr8:105291143..105291166
-
Hg19::chr8:12898422..12898427,-p@chr8:12898422..12898427
-
Hg19::chr8:12999595..12999600,+p@chr8:12999595..12999600
+
Hg19::chr8:13199276..13199284,+p@chr8:13199276..13199284
+
Hg19::chr8:13199316..13199325,+p@chr8:13199316..13199325
+
Hg19::chr8:13526697..13526704,+p@chr8:13526697..13526704
+
Hg19::chr8:138082720..138082726,-p@chr8:138082720..138082726
-
Hg19::chr8:22559267..22559271,-p@chr8:22559267..22559271
-
Hg19::chr8:86174690..86174727,+p@chr8:86174690..86174727
+
Hg19::chr9:124116019..124116044,-p@chr9:124116019..124116044
-
Hg19::chr9:124116047..124116052,-p@chr9:124116047..124116052
-
Hg19::chr9:124632999..124633011,-p@chr9:124632999..124633011
-
Hg19::chr9:35194941..35194952,-p@chr9:35194941..35194952
-
Hg19::chr9:80847589..80847596,-p@chr9:80847589..80847596
-
Hg19::chrX:46811494..46811522,-p@chrX:46811494..46811522
-
Hg19::chrX:71093307..71093345,-p@chrX:71093307..71093345
-


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:0016323basolateral plasma membrane0.0201253396018479
GO:0001672regulation of chromatin assembly or disassembly0.0201253396018479
GO:0015460transport accessory protein activity0.0201253396018479
GO:0048260positive regulation of receptor-mediated endocytosis0.0201253396018479
GO:0030121AP-1 adaptor complex0.0201253396018479
GO:0030669clathrin-coated endocytic vesicle membrane0.0201253396018479
GO:0030128clathrin coat of endocytic vesicle0.0201253396018479
GO:0030122AP-2 adaptor complex0.0201253396018479
GO:0005522profilin binding0.0201253396018479
GO:0001784phosphotyrosine binding0.0201253396018479
GO:0045309protein phosphorylated amino acid binding0.0201253396018479
GO:0030666endocytic vesicle membrane0.0201253396018479
GO:0045334clathrin-coated endocytic vesicle0.0201253396018479
GO:0048259regulation of receptor-mediated endocytosis0.0201253396018479
GO:0051219phosphoprotein binding0.0268120729752947
GO:0030276clathrin binding0.0268120729752947
GO:0043393regulation of protein binding0.0268120729752947
GO:0030132clathrin coat of coated pit0.0268120729752947
GO:0042632cholesterol homeostasis0.0268120729752947
GO:0055092sterol homeostasis0.0268120729752947
GO:0045178basal part of cell0.0268120729752947
GO:0009925basal plasma membrane0.0268120729752947
GO:0030130clathrin coat of trans-Golgi network vesicle0.0268120729752947
GO:0055088lipid homeostasis0.0268120729752947
GO:0045807positive regulation of endocytosis0.0268120729752947
GO:0012510trans-Golgi network transport vesicle membrane0.0268120729752947
GO:0030159receptor signaling complex scaffold activity0.0268120729752947
GO:0017124SH3 domain binding0.0277325453196628
GO:0032947protein complex scaffold0.0277325453196628
GO:0030125clathrin vesicle coat0.0280204918071434
GO:0030139endocytic vesicle0.0280204918071434
GO:0005829cytosol0.0280204918071434
GO:0030665clathrin coated vesicle membrane0.0280204918071434
GO:0051098regulation of binding0.0330964323601507
GO:0030140trans-Golgi network transport vesicle0.0332966133538596
GO:0030658transport vesicle membrane0.0338330086151013
GO:0065009regulation of a molecular function0.0338330086151013
GO:0030660Golgi-associated vesicle membrane0.0338330086151013
GO:0030100regulation of endocytosis0.0341451676617017
GO:0005925focal adhesion0.0341451676617017
GO:0007292female gamete generation0.03428961072765
GO:0005924cell-substrate adherens junction0.0350245552621578
GO:0051050positive regulation of transport0.0350245552621578
GO:0030027lamellipodium0.0350245552621578
GO:0030055cell-matrix junction0.0350245552621578
GO:0007015actin filament organization0.0350245552621578
GO:0006898receptor-mediated endocytosis0.0350245552621578
GO:0005905coated pit0.0359625052134099
GO:0006919caspase activation0.0376780663092173
GO:0051052regulation of DNA metabolic process0.0378523782391324
GO:0005769early endosome0.0378523782391324
GO:0030120vesicle coat0.0378523782391324
GO:0043280positive regulation of caspase activity0.0378523782391324
GO:0030662coated vesicle membrane0.0378916483779762
GO:0030131clathrin adaptor complex0.0380005712279603
GO:0005912adherens junction0.0380005712279603
GO:0030119AP-type membrane coat adaptor complex0.0380005712279603
GO:0043281regulation of caspase activity0.0414500800115022
GO:0008154actin polymerization and/or depolymerization0.0414500800115022
GO:0030133transport vesicle0.0420894203107372
GO:0030118clathrin coat0.0433612596610362
GO:0005798Golgi-associated vesicle0.0445912181473384
GO:0031252leading edge0.04507972218143
GO:0012505endomembrane system0.04507972218143
GO:0008022protein C-terminus binding0.0455984987589061
GO:0051345positive regulation of hydrolase activity0.0461145460520442
GO:0008203cholesterol metabolic process0.0466148382190784
GO:0043229intracellular organelle0.0466526491276922
GO:0043226organelle0.0466526491276922
GO:0016043cellular component organization and biogenesis0.0467027924574183



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>

Cell Type
Ontology termp-valuen
lymphocyte of B lineage1.01e-0924
pro-B cell1.01e-0924
Disease
Ontology termp-valuen
anemia5.42e-1951
hematopoietic system disease1.55e-982
cardiovascular system disease3.10e-504
lymphoma3.81e-2110


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)
MA0003.11.23198e-09
MA0004.11.57354
MA0006.10.0549193
MA0007.10.15812
MA0009.10.0921642
MA0014.18.79198e-07
MA0017.10.169824
MA0019.10.145911
MA0024.10.0539327
MA0025.10.156731
MA0027.11.42991
MA0028.10.00402772
MA0029.10.473997
MA0030.10.0564002
MA0031.10.149825
MA0038.11.20486
MA0040.10.0620643
MA0041.10.0142783
MA0042.10.00136332
MA0043.10.0922966
MA0046.10.0876606
MA0048.10.116237
MA0050.10.289446
MA0051.10.381857
MA0052.10.063373
MA0055.10.254158
MA0056.10
MA0057.10.0159899
MA0058.11.15615
MA0059.10.899343
MA0060.12.26891
MA0061.12.02939
MA0063.10
MA0066.10.0360864
MA0067.10.27074
MA0068.10.0593753
MA0069.11.51389
MA0070.10.58544
MA0071.10.166693
MA0072.10.974231
MA0073.11.86107e-11
MA0074.10.100064
MA0076.10.000399824
MA0077.10.0769176
MA0078.10.39005
MA0081.10.129271
MA0083.10.0953407
MA0084.10.409533
MA0087.10.0789333
MA0088.13.57501
MA0089.10
MA0090.10.0982188
MA0091.10.501238
MA0092.10.239454
MA0093.12.33941
MA0095.10
MA0098.10
MA0100.10.00783907
MA0101.11.20117
MA0103.11.5752
MA0105.11.09282
MA0106.10.494419
MA0107.12.89703
MA0108.20.964479
MA0109.10
MA0111.10.333994
MA0113.10.158907
MA0114.10.15612
MA0115.10.220284
MA0116.10.0348037
MA0117.10.108632
MA0119.10.432231
MA0122.10.120782
MA0124.11.07741
MA0125.10.883082
MA0130.10
MA0131.10.0201412
MA0132.10
MA0133.10
MA0135.11.69284
MA0136.10.00727027
MA0139.10.317558
MA0140.10.300029
MA0141.10.126458
MA0142.12.19002
MA0143.10.538664
MA0144.10.189056
MA0145.10.272693
MA0146.10.000268806
MA0147.10.520905
MA0148.10.579045
MA0149.10.150981
MA0062.20.00115758
MA0035.20.162321
MA0039.20.000115446
MA0138.20.202643
MA0002.21.56067
MA0137.20.0148856
MA0104.20.881271
MA0047.20.130169
MA0112.22.62702e-05
MA0065.20.0702048
MA0150.10.427358
MA0151.10
MA0152.10.3138
MA0153.10.138305
MA0154.11.20292
MA0155.10.0529497
MA0156.10.00483111
MA0157.10.106284
MA0158.10
MA0159.10.278725
MA0160.11.18436
MA0161.10
MA0162.11.09684e-09
MA0163.18.58586e-06
MA0164.10.341535
MA0080.20.279073
MA0018.20.143387
MA0099.21.35149
MA0079.20
MA0102.20.439224
MA0258.10.00711908
MA0259.10.570514
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
EBF1#1879221.902352141985610.002192958218885880.0126403423711144



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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C169&oldid=3067287"