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Coexpression cluster:C158: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 10:45, 17 September 2013


Full id: C158_adrenal_gastric_temporal_parietal_duodenum_caudate_putamen



Phase1 CAGE Peaks

Hg19::chr10:10836699..10836711,-p10@SFTA1P
Hg19::chr10:10836739..10836753,-p8@SFTA1P
Hg19::chr10:36988176..36988178,-p@chr10:36988176..36988178
-
Hg19::chr10:37004821..37004852,-p@chr10:37004821..37004852
-
Hg19::chr10:90305239..90305251,-p10@RNLS
Hg19::chr12:78227833..78227840,-p@chr12:78227833..78227840
-
Hg19::chr12:86272170..86272176,+p@chr12:86272170..86272176
+
Hg19::chr12:91218399..91218404,+p@chr12:91218399..91218404
+
Hg19::chr13:67730380..67730387,+p@chr13:67730380..67730387
+
Hg19::chr13:69251442..69251477,+p@chr13:69251442..69251477
+
Hg19::chr13:69259745..69259757,-p@chr13:69259745..69259757
-
Hg19::chr13:80914790..80914795,-p41@SPRY2
Hg19::chr13:90020369..90020372,-p@chr13:90020369..90020372
-
Hg19::chr14:47289600..47289605,-p@chr14:47289600..47289605
-
Hg19::chr14:47289641..47289643,-p@chr14:47289641..47289643
-
Hg19::chr14:47289644..47289662,-p@chr14:47289644..47289662
-
Hg19::chr14:85978533..85978538,-p@chr14:85978533..85978538
-
Hg19::chr15:36251080..36251084,-p@chr15:36251080..36251084
-
Hg19::chr16:16593388..16593394,+p@chr16:16593388..16593394
+
Hg19::chr16:68014345..68014352,-p1@AB590471
Hg19::chr16:68014358..68014363,-p3@DPEP3
Hg19::chr16:68014368..68014384,-p2@DPEP3
Hg19::chr16:68014387..68014423,-p1@DPEP3
Hg19::chr19:14444525..14444559,+p1@uc002myk.2
Hg19::chr1:218214846..218214850,-p@chr1:218214846..218214850
-
Hg19::chr1:218221538..218221546,-p@chr1:218221538..218221546
-
Hg19::chr1:218222265..218222274,-p@chr1:218222265..218222274
-
Hg19::chr1:218388686..218388689,-p@chr1:218388686..218388689
-
Hg19::chr1:82934455..82934461,-p@chr1:82934455..82934461
-
Hg19::chr1:82951436..82951474,-p@chr1:82951436..82951474
-
Hg19::chr1:84326618..84326622,-p1@ENST00000417565
Hg19::chr21:21703199..21703203,-p@chr21:21703199..21703203
-
Hg19::chr21:21823911..21823933,+p@chr21:21823911..21823933
+
Hg19::chr21:23058648..23058654,-p1@ENST00000416182
Hg19::chr21:23066072..23066082,+p@chr21:23066072..23066082
+
Hg19::chr21:23066147..23066153,+p@chr21:23066147..23066153
+
Hg19::chr21:23120868..23120880,+p@chr21:23120868..23120880
+
Hg19::chr21:23650444..23650446,+p@chr21:23650444..23650446
+
Hg19::chr2:132300828..132300841,-p1@uc002ttc.1
Hg19::chr2:150961763..150961789,-p@chr2:150961763..150961789
-
Hg19::chr2:150961910..150961916,-p@chr2:150961910..150961916
-
Hg19::chr2:150969651..150969663,+p@chr2:150969651..150969663
+
Hg19::chr2:150969704..150969713,+p@chr2:150969704..150969713
+
Hg19::chr2:150969742..150969756,+p@chr2:150969742..150969756
+
Hg19::chr2:150978421..150978425,+p@chr2:150978421..150978425
+
Hg19::chr2:187685152..187685168,-p@chr2:187685152..187685168
-
Hg19::chr2:187685199..187685210,-p@chr2:187685199..187685210
-
Hg19::chr2:77315799..77315830,+p@chr2:77315799..77315830
+
Hg19::chr3:146962974..146962979,-p@chr3:146962974..146962979
-
Hg19::chr3:147450214..147450243,-p@chr3:147450214..147450243
-
Hg19::chr3:147869637..147869641,+p@chr3:147869637..147869641
+
Hg19::chr3:161200616..161200619,+p@chr3:161200616..161200619
+
Hg19::chr3:174950074..174950087,-p@chr3:174950074..174950087
-
Hg19::chr3:174950099..174950115,-p@chr3:174950099..174950115
-
Hg19::chr3:175131802..175131807,-p@chr3:175131802..175131807
-
Hg19::chr3:181328302..181328339,+p4@SOX2-OT
Hg19::chr3:181328346..181328351,+p22@SOX2-OT
Hg19::chr3:181328363..181328382,+p5@SOX2-OT
Hg19::chr3:181328387..181328399,+p16@SOX2-OT
Hg19::chr3:181328459..181328465,+p27@SOX2-OT
Hg19::chr3:181328472..181328478,+p25@SOX2-OT
Hg19::chr3:181328499..181328502,+p32@SOX2-OT
Hg19::chr3:190580437..190580450,-p1@GMNC
Hg19::chr3:190580477..190580489,-p2@GMNC
Hg19::chr3:190999899..190999913,-p10@UTS2D
Hg19::chr3:190999916..190999925,-p13@UTS2D
Hg19::chr3:190999951..190999959,-p15@UTS2D
Hg19::chr3:191000039..191000046,-p9@UTS2D
Hg19::chr3:191047287..191047298,+p11@CCDC50
Hg19::chr3:85553584..85553599,-p@chr3:85553584..85553599
-
Hg19::chr3:85553737..85553767,+p1@AB646740
p1@AB646741
p1@AB646742
p1@AB646743
Hg19::chr4:34336968..34336974,-p@chr4:34336968..34336974
-
Hg19::chr4:34480309..34480321,-p@chr4:34480309..34480321
-
Hg19::chr4:35102522..35102546,+p@chr4:35102522..35102546
+
Hg19::chr4:35107931..35107966,+p@chr4:35107931..35107966
+
Hg19::chr4:67618078..67618083,-p@chr4:67618078..67618083
-
Hg19::chr4:67651552..67651563,+p@chr4:67651552..67651563
+
Hg19::chr5:103573467..103573478,+p@chr5:103573467..103573478
+
Hg19::chr5:103625303..103625326,+p@chr5:103625303..103625326
+
Hg19::chr5:28339690..28339727,-p@chr5:28339690..28339727
-
Hg19::chr5:92020578..92020613,-p@chr5:92020578..92020613
-
Hg19::chr5:92023982..92024005,-p4@ENST00000503489
Hg19::chr5:92024011..92024031,-p3@ENST00000503489
Hg19::chr5:92179437..92179443,+p@chr5:92179437..92179443
+
Hg19::chr6:113369869..113369877,+p@chr6:113369869..113369877
+
Hg19::chr6:113454693..113454704,+p@chr6:113454693..113454704
+
Hg19::chr6:122216918..122216922,-p@chr6:122216918..122216922
-
Hg19::chr6:122409629..122409642,-p@chr6:122409629..122409642
-
Hg19::chr6:94129263..94129284,-p1@EPHA7
Hg19::chr6:94129519..94129544,+p@chr6:94129519..94129544
+
Hg19::chr6:94845210..94845215,+p@chr6:94845210..94845215
+
Hg19::chr7:111033178..111033202,-p11@IMMP2L
Hg19::chr7:111051726..111051739,-p@chr7:111051726..111051739
-
Hg19::chr7:111051766..111051788,-p@chr7:111051766..111051788
-
Hg19::chr7:111051794..111051815,-p@chr7:111051794..111051815
-
Hg19::chr7:111051818..111051822,-p@chr7:111051818..111051822
-
Hg19::chr7:111054273..111054319,-p@chr7:111054273..111054319
-
Hg19::chr7:15802479..15802491,+p@chr7:15802479..15802491
+
Hg19::chr7:15802505..15802513,+p@chr7:15802505..15802513
+
Hg19::chr7:80824380..80824393,+p@chr7:80824380..80824393
+
Hg19::chr8:115584851..115584862,+p@chr8:115584851..115584862
+
Hg19::chr8:115584867..115584882,+p@chr8:115584867..115584882
+
Hg19::chr8:130152310..130152315,+p@chr8:130152310..130152315
+
Hg19::chr8:59953375..59953393,-p@chr8:59953375..59953393
-
Hg19::chr9:13323362..13323373,-p1@ENST00000433817
Hg19::chr9:30925323..30925363,-p@chr9:30925323..30925363
-
Hg19::chrX:13062752..13062771,-p2@FAM9C
Hg19::chrX:134975753..134975758,+p2@SAGE1
Hg19::chrX:2291152..2291163,-p@chrX:2291152..2291163
-


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:0042720mitochondrial inner membrane peptidase complex0.0130478988412968
GO:0004244mitochondrial inner membrane peptidase activity0.0130478988412968
GO:0050954sensory perception of mechanical stimulus0.0130478988412968
GO:0007605sensory perception of sound0.0130478988412968
GO:0006627mitochondrial protein processing0.0138454744697207
GO:0004237membrane dipeptidase activity0.0230717153481549



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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adrenal gland2.39e-663
adrenal cortex2.39e-663
adrenal/interrenal gland2.39e-663
cortex1.22e-1415
intermediate mesoderm1.52e-0828
endocrine gland4.03e-0735
Disease
Ontology termp-valuen
adenocarcinoma2.15e-0925


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)
MA0003.13.8441e-12
MA0004.10.2727
MA0006.10.018185
MA0007.10.547942
MA0009.10.282037
MA0014.12.12898e-09
MA0017.10.337188
MA0019.10.450068
MA0024.10.0472324
MA0025.10.144229
MA0027.11.4058
MA0028.10.169788
MA0029.11.16259
MA0030.10.0495036
MA0031.10.31224
MA0038.11.43546
MA0040.10.444381
MA0041.11.23902
MA0042.11.99885
MA0043.10.0829567
MA0046.10.0786003
MA0048.10.00316068
MA0050.10.000989088
MA0051.10.0280486
MA0052.10.204999
MA0055.10.00013321
MA0056.10
MA0057.10.00104939
MA0058.10.595195
MA0059.10.286272
MA0060.17.41488
MA0061.10.158707
MA0063.10
MA0066.10.0052822
MA0067.10.708096
MA0068.10.000126314
MA0069.10.266146
MA0070.10.922033
MA0071.10.64729
MA0072.10.249695
MA0073.10
MA0074.10.184146
MA0076.10.336869
MA0077.11.85451
MA0078.10.581654
MA0081.10.286731
MA0083.11.51125
MA0084.10.390659
MA0087.10.902554
MA0088.10.0324301
MA0089.10
MA0090.10.249275
MA0091.10.0315262
MA0092.10.200484
MA0093.10.468647
MA0095.10
MA0098.10
MA0100.10.0335784
MA0101.10.235856
MA0103.11.14669
MA0105.10.0394591
MA0106.10.253333
MA0107.10.394003
MA0108.20.890202
MA0109.10
MA0111.10.0919968
MA0113.10.481762
MA0114.10.492633
MA0115.10.205538
MA0116.10.137413
MA0117.10.324405
MA0119.10.364115
MA0122.10.355054
MA0124.10.533548
MA0125.10.135009
MA0130.10
MA0131.10.0167544
MA0132.10
MA0133.10
MA0135.10.651619
MA0136.10.201028
MA0139.10.00779383
MA0140.11.52236
MA0141.10.00686993
MA0142.10.797666
MA0143.10.280953
MA0144.10.144918
MA0145.10.189376
MA0146.18.64428e-06
MA0147.10.313879
MA0148.10.984952
MA0149.10.126959
MA0062.20.0197443
MA0035.21.88704
MA0039.25.15009e-08
MA0138.20.585078
MA0002.20.0983344
MA0137.20.183829
MA0104.20.182621
MA0047.20.920931
MA0112.20.00183496
MA0065.20.0178654
MA0150.10.235498
MA0151.10
MA0152.10.271835
MA0153.10.126593
MA0154.10.000153354
MA0155.10.00426527
MA0156.10.188917
MA0157.10.230279
MA0158.10
MA0159.10.00462996
MA0160.10.561013
MA0161.10
MA0162.19.23289e-09
MA0163.12.88534e-07
MA0164.10.302268
MA0080.20.0431684
MA0018.20.123028
MA0099.20.0202533
MA0079.20
MA0102.20.419911
MA0258.10.184176
MA0259.10.165553
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

No analysis results for this cluster

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

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