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Coexpression cluster:C126: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 10:37, 17 September 2013


Full id: C126_gastrointestinal_argyrophil_smallcell_merkel_bile_insula_brain



Phase1 CAGE Peaks

Hg19::chr10:102055183..102055184,-p@chr10:102055183..102055184
-
Hg19::chr10:102089952..102089973,-p2@PKD2L1
Hg19::chr10:102089977..102089990,-p1@PKD2L1
Hg19::chr10:102207688..102207707,+p@chr10:102207688..102207707
+
Hg19::chr10:16562454..16562494,+p@chr10:16562454..16562494
+
Hg19::chr10:16562497..16562508,+p@chr10:16562497..16562508
+
Hg19::chr10:16563117..16563150,-p5@C1QL3
Hg19::chr10:76801606..76801607,+p@chr10:76801606..76801607
+
Hg19::chr12:52055874..52055911,+p@chr12:52055874..52055911
+
Hg19::chr12:52081218..52081224,+p@chr12:52081218..52081224
+
Hg19::chr12:53596603..53596614,+p@chr12:53596603..53596614
+
Hg19::chr12:53596669..53596685,+p@chr12:53596669..53596685
+
Hg19::chr12:58838512..58838558,+p@chr12:58838512..58838558
+
Hg19::chr12:59095448..59095488,-p@chr12:59095448..59095488
-
Hg19::chr12:81771814..81771826,+p1@ENST00000546936
Hg19::chr12:81771827..81771839,+p2@ENST00000546936
Hg19::chr12:81776004..81776007,+p@chr12:81776004..81776007
+
Hg19::chr12:81813961..81813970,+p@chr12:81813961..81813970
+
Hg19::chr13:86221801..86221809,+p@chr13:86221801..86221809
+
Hg19::chr13:86221845..86221851,+p@chr13:86221845..86221851
+
Hg19::chr13:92981567..92981607,-p@chr13:92981567..92981607
-
Hg19::chr13:93057493..93057501,-p@chr13:93057493..93057501
-
Hg19::chr13:93057514..93057522,-p@chr13:93057514..93057522
-
Hg19::chr14:93383646..93383662,-p@chr14:93383646..93383662
-
Hg19::chr14:93397768..93397779,+p4@CHGA
Hg19::chr14:93398754..93398767,+p2@BC106953
Hg19::chr15:46428206..46428211,-p@chr15:46428206..46428211
-
Hg19::chr15:46545564..46545574,-p@chr15:46545564..46545574
-
Hg19::chr16:19663104..19663118,+p@chr16:19663104..19663118
+
Hg19::chr16:19663125..19663134,+p@chr16:19663125..19663134
+
Hg19::chr16:57640925..57640941,-p@chr16:57640925..57640941
-
Hg19::chr17:39565033..39565073,-p@chr17:39565033..39565073
-
Hg19::chr17:39565125..39565132,-p@chr17:39565125..39565132
-
Hg19::chr17:43053755..43053784,+p@chr17:43053755..43053784
+
Hg19::chr17:46303368..46303374,+p@chr17:46303368..46303374
+
Hg19::chr17:46303468..46303475,+p@chr17:46303468..46303475
+
Hg19::chr18:40194793..40194820,+p@chr18:40194793..40194820
+
Hg19::chr18:40194830..40194841,+p@chr18:40194830..40194841
+
Hg19::chr18:42380070..42380105,+p@chr18:42380070..42380105
+
Hg19::chr19:35940486..35940504,+p2@FFAR2
Hg19::chr19:36347787..36347850,+p1@KIRREL2
Hg19::chr19:42656683..42656689,+p1@ENST00000559786
p1@uc002ost.1
Hg19::chr19:45417574..45417589,+p1@APOC1
Hg19::chr1:31924907..31924925,-p@chr1:31924907..31924925
-
Hg19::chr1:31944306..31944336,-p@chr1:31944306..31944336
-
Hg19::chr1:31975103..31975114,+p@chr1:31975103..31975114
+
Hg19::chr1:32013141..32013146,+p27@TINAGL1
Hg19::chr1:95846540..95846548,-p2@ENST00000426881
p2@uc001drj.1
p2@uc001drk.1
Hg19::chr1:95846559..95846566,-p1@ENST00000426881
p1@uc001drj.1
p1@uc001drk.1
Hg19::chr1:98514995..98515010,-p9@MIR137HG
Hg19::chr1:98515017..98515065,-p3@MIR137HG
Hg19::chr20:22464921..22464928,-p@chr20:22464921..22464928
-
Hg19::chr20:44048281..44048327,-p@chr20:44048281..44048327
-
Hg19::chr20:44048705..44048721,+p19@PIGT
Hg19::chr20:47299359..47299377,-p@chr20:47299359..47299377
-
Hg19::chr21:45905448..45905455,+p1@ENST00000449713
Hg19::chr22:26299513..26299521,+p@chr22:26299513..26299521
+
Hg19::chr22:26299554..26299556,+p@chr22:26299554..26299556
+
Hg19::chr22:26299576..26299591,+p@chr22:26299576..26299591
+
Hg19::chr22:26299595..26299605,+p@chr22:26299595..26299605
+
Hg19::chr22:26299607..26299623,+p@chr22:26299607..26299623
+
Hg19::chr2:103969385..103969401,+p@chr2:103969385..103969401
+
Hg19::chr2:105030478..105030489,-p1@ENST00000449772
Hg19::chr2:128180446..128180455,+p8@PROC
Hg19::chr2:158443765..158443789,-p@chr2:158443765..158443789
-
Hg19::chr2:158443804..158443809,-p@chr2:158443804..158443809
-
Hg19::chr2:163194011..163194032,+p@chr2:163194011..163194032
+
Hg19::chr3:157823323..157823328,+p17@RSRC1
Hg19::chr3:157824156..157824164,-p4@SHOX2
Hg19::chr3:157824202..157824211,-p3@SHOX2
Hg19::chr3:157824322..157824334,-p7@SHOX2
Hg19::chr3:157824341..157824356,-p8@SHOX2
Hg19::chr3:157824437..157824459,-p5@SHOX2
Hg19::chr3:157825104..157825109,-p@chr3:157825104..157825109
-
Hg19::chr3:183947366..183947381,+p@chr3:183947366..183947381
+
Hg19::chr3:183947382..183947395,+p@chr3:183947382..183947395
+
Hg19::chr3:183948136..183948147,+p2@VWA5B2
Hg19::chr3:183948161..183948173,+p1@VWA5B2
Hg19::chr3:24206665..24206674,-p21@THRB
Hg19::chr3:55187389..55187391,-p@chr3:55187389..55187391
-
Hg19::chr3:55313580..55313599,-p@chr3:55313580..55313599
-
Hg19::chr3:59035577..59035598,-p3@C3orf67
Hg19::chr4:140762693..140762699,-p@chr4:140762693..140762699
-
Hg19::chr4:147558115..147558117,-p@chr4:147558115..147558117
-
Hg19::chr4:147558642..147558652,-p@chr4:147558642..147558652
-
Hg19::chr4:147559302..147559313,+p@chr4:147559302..147559313
+
Hg19::chr4:182186203..182186217,-p1@ENST00000512547
Hg19::chr4:90185426..90185448,+p@chr4:90185426..90185448
+
Hg19::chr5:115890554..115890570,-p11@SEMA6A
Hg19::chr5:140220769..140220797,+p1@PCDHA8
Hg19::chr5:147365729..147365732,-p@chr5:147365729..147365732
-
Hg19::chr5:35238029..35238052,-p@chr5:35238029..35238052
-
Hg19::chr5:7078237..7078241,-p@chr5:7078237..7078241
-
Hg19::chr5:85440032..85440036,-p@chr5:85440032..85440036
-
Hg19::chr5:85654384..85654387,-p@chr5:85654384..85654387
-
Hg19::chr5:85698439..85698441,-p@chr5:85698439..85698441
-
Hg19::chr5:85726548..85726552,-p@chr5:85726548..85726552
-
Hg19::chr5:85758220..85758224,-p@chr5:85758220..85758224
-
Hg19::chr5:85866603..85866622,-p@chr5:85866603..85866622
-
Hg19::chr6:102247584..102247620,+p@chr6:102247584..102247620
+
Hg19::chr6:2431114..2431122,+p@chr6:2431114..2431122
+
Hg19::chr6:25703371..25703392,-p@chr6:25703371..25703392
-
Hg19::chr6:25703430..25703438,-p@chr6:25703430..25703438
-
Hg19::chr6:52591707..52591712,+p@chr6:52591707..52591712
+
Hg19::chr7:10279440..10279456,-p@chr7:10279440..10279456
-
Hg19::chr7:10279467..10279477,-p@chr7:10279467..10279477
-
Hg19::chr7:119341438..119341443,-p@chr7:119341438..119341443
-
Hg19::chr7:119432715..119432719,-p@chr7:119432715..119432719
-
Hg19::chr7:119434164..119434168,-p@chr7:119434164..119434168
-
Hg19::chr7:141840592..141840632,+p@chr7:141840592..141840632
+
Hg19::chr7:19417679..19417693,+p@chr7:19417679..19417693
+
Hg19::chr7:19417700..19417718,+p@chr7:19417700..19417718
+
Hg19::chr7:25476780..25476790,+p@chr7:25476780..25476790
+
Hg19::chr7:25476805..25476814,+p@chr7:25476805..25476814
+
Hg19::chr7:27135418..27135419,-p6@HOXA1
Hg19::chr8:61496517..61496522,+p30@RAB2A
Hg19::chr8:61761056..61761069,+p@chr8:61761056..61761069
+
Hg19::chr8:61761479..61761510,+p@chr8:61761479..61761510
+
Hg19::chr8:83522938..83522947,-p@chr8:83522938..83522947
-
Hg19::chr8:83570383..83570385,-p@chr8:83570383..83570385
-
Hg19::chr8:83573739..83573746,-p@chr8:83573739..83573746
-
Hg19::chr8:83574464..83574473,-p@chr8:83574464..83574473
-
Hg19::chr8:83603164..83603178,-p@chr8:83603164..83603178
-
Hg19::chr8:83603186..83603195,-p@chr8:83603186..83603195
-
Hg19::chr9:104500249..104500268,-p1@AB385519
Hg19::chr9:104500922..104500940,-p1@GRIN3A
Hg19::chr9:105186923..105186932,+p@chr9:105186923..105186932
+
Hg19::chr9:105186934..105186953,+p@chr9:105186934..105186953
+
Hg19::chr9:105186978..105186981,+p@chr9:105186978..105186981
+
Hg19::chr9:109984515..109984523,+p@chr9:109984515..109984523
+
Hg19::chr9:136754716..136754724,-p@chr9:136754716..136754724
-
Hg19::chr9:18777363..18777375,-p@chr9:18777363..18777375
-
Hg19::chr9:18777378..18777385,-p@chr9:18777378..18777385
-
Hg19::chr9:74802300..74802309,+p@chr9:74802300..74802309
+
Hg19::chr9:9687992..9688006,+p@chr9:9687992..9688006
+
Hg19::chr9:9688031..9688053,+p@chr9:9688031..9688053
+
Hg19::chrX:122447934..122447944,-p@chrX:122447934..122447944
-
Hg19::chrX:122447968..122447983,-p@chrX:122447968..122447983
-
Hg19::chrX:33744981..33744990,-p@chrX:33744981..33744990
-
Hg19::chrX:33745016..33745027,-p@chrX:33745016..33745027
-
Hg19::chrX:83993981..83993987,+p@chrX:83993981..83993987
+


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:0032501multicellular organismal process0.0323796067349582
GO:0007399nervous system development0.0323796067349582
GO:0005509calcium ion binding0.0323796067349582
GO:0003808protein C (activated) activity0.0323796067349582
GO:0042157lipoprotein metabolic process0.0389844058753471



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><br>disease_data<br>

Disease
Ontology termp-valuen
gastrointestinal system cancer1.43e-1514


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)
MA0003.14.57573e-14
MA0004.10.310213
MA0006.10.00760704
MA0007.10.260564
MA0009.10.403855
MA0014.10.000699458
MA0017.10.283512
MA0019.10.852885
MA0024.10.249365
MA0025.10.0941998
MA0027.11.29654
MA0028.10.0013091
MA0029.10.511151
MA0030.11.13957
MA0031.10.890975
MA0038.10.17039
MA0040.10.0283962
MA0041.10.524881
MA0042.10.274153
MA0043.10.404372
MA0046.14.48606
MA0048.10.306631
MA0050.10.173403
MA0051.10.444816
MA0052.11.66148
MA0055.14.41333
MA0056.10
MA0057.10.0906738
MA0058.10.10618
MA0059.10.370082
MA0060.10.0117433
MA0061.10.0156668
MA0063.10
MA0066.10.295007
MA0067.10.186693
MA0068.10.140826
MA0069.10.0435858
MA0070.10.362367
MA0071.12.61866
MA0072.10.994867
MA0073.18.68653e-08
MA0074.10.0323191
MA0076.10.00171159
MA0077.10.969146
MA0078.11.0871
MA0081.10.506733
MA0083.10.416241
MA0084.10.83174
MA0087.10.351605
MA0088.10.00798431
MA0089.10
MA0090.10.157721
MA0091.18.65188
MA0092.11.5995
MA0093.10.256795
MA0095.10
MA0098.10
MA0100.10.0116121
MA0101.10.00888122
MA0103.11.04657
MA0105.10.0164424
MA0106.10.592902
MA0107.10.0789023
MA0108.20.586024
MA0109.10
MA0111.10.565646
MA0113.11.54761
MA0114.10.162173
MA0115.10.144573
MA0116.10.0521326
MA0117.10.21381
MA0119.10.213088
MA0122.10.513571
MA0124.10.391442
MA0125.11.02559
MA0130.10
MA0131.10.034219
MA0132.10
MA0133.10
MA0135.10.791371
MA0136.10.180848
MA0139.10.262851
MA0140.11.51175
MA0141.10.655887
MA0142.10.299627
MA0143.10.266522
MA0144.10.0297148
MA0145.10.0929044
MA0146.18.69383e-06
MA0147.10.0034711
MA0148.11.53416
MA0149.10.000605517
MA0062.20.00150189
MA0035.21.50635
MA0039.24.02416e-10
MA0138.20.545684
MA0002.20.202468
MA0137.20.0128927
MA0104.20.00102978
MA0047.21.3617
MA0112.20.000195663
MA0065.20.136144
MA0150.10.341072
MA0151.10
MA0152.11.56239
MA0153.13.99813
MA0154.11.70962
MA0155.10.00155059
MA0156.10.0296378
MA0157.10.442339
MA0158.10
MA0159.10.0922579
MA0160.10.827863
MA0161.10
MA0162.16.08417e-08
MA0163.10.0261499
MA0164.10.289875
MA0080.20.257089
MA0018.20.125708
MA0099.20.124423
MA0079.20
MA0102.20.335846
MA0258.10.0228062
MA0259.10.0213588
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
SUZ12#2351293.198879632621040.002206406774237920.0127087423943655



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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