Personal tools

Coexpression cluster:C253

From FANTOM5_SSTAR

Revision as of 11:06, 17 September 2013 by Autoedit (talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


Full id: C253_spleen_rhabdomyosarcoma_Hepatocyte_small_uterus_liver_rectum



Phase1 CAGE Peaks

Hg19::chr10:102890846..102890877,+p2@TLX1
Hg19::chr10:102890890..102890902,-p1@TLX1NB
Hg19::chr10:102891023..102891028,+p7@TLX1
Hg19::chr10:102891044..102891047,+p6@TLX1
Hg19::chr10:102891048..102891078,+p1@TLX1
Hg19::chr10:102891168..102891197,+p3@TLX1
Hg19::chr10:102900211..102900229,-p@chr10:102900211..102900229
-
Hg19::chr10:125823416..125823426,-p@chr10:125823416..125823426
-
Hg19::chr11:114042566..114042569,+p@chr11:114042566..114042569
+
Hg19::chr11:56859603..56859606,-p@chr11:56859603..56859606
-
Hg19::chr11:56859608..56859619,-p@chr11:56859608..56859619
-
Hg19::chr11:56859638..56859643,-p@chr11:56859638..56859643
-
Hg19::chr11:56859693..56859701,-p@chr11:56859693..56859701
-
Hg19::chr11:56859722..56859732,-p@chr11:56859722..56859732
-
Hg19::chr11:72350972..72350982,+p@chr11:72350972..72350982
+
Hg19::chr11:72350992..72351010,+p@chr11:72350992..72351010
+
Hg19::chr11:925438..925445,+p20@AP2A2
Hg19::chr12:103981044..103981061,+p1@STAB2
Hg19::chr12:52809084..52809091,+p@chr12:52809084..52809091
+
Hg19::chr14:73702509..73702520,+p@chr14:73702509..73702520
+
Hg19::chr15:101999172..101999221,-p@chr15:101999172..101999221
-
Hg19::chr15:94899150..94899178,+p5@MCTP2
Hg19::chr15:94899183..94899200,+p7@MCTP2
Hg19::chr15:95561320..95561328,-p@chr15:95561320..95561328
-
Hg19::chr15:95561338..95561347,-p@chr15:95561338..95561347
-
Hg19::chr15:95561349..95561361,-p@chr15:95561349..95561361
-
Hg19::chr16:199450..199454,+p@chr16:199450..199454
+
Hg19::chr16:70624024..70624042,+p@chr16:70624024..70624042
+
Hg19::chr16:84218794..84218800,+p@chr16:84218794..84218800
+
Hg19::chr17:78171885..78171900,+p@chr17:78171885..78171900
+
Hg19::chr19:17729847..17729880,-p5@UNC13A
Hg19::chr19:32401253..32401271,-p@chr19:32401253..32401271
-
Hg19::chr19:32401274..32401289,-p@chr19:32401274..32401289
-
Hg19::chr19:496478..496490,+p3@MADCAM1
Hg19::chr1:159172187..159172197,-p1@uc001ftm.1
Hg19::chr1:28520450..28520453,-p21@PTAFR
Hg19::chr1:91921807..91921821,+p@chr1:91921807..91921821
+
Hg19::chr21:40459334..40459341,+p@chr21:40459334..40459341
+
Hg19::chr2:96922657..96922663,-p@chr2:96922657..96922663
-
Hg19::chr3:130267501..130267516,+p@chr3:130267501..130267516
+
Hg19::chr3:183145802..183145813,-p23@MCF2L2
Hg19::chr3:46505111..46505126,-p3@LTF
Hg19::chr4:53811826..53811839,+p1@ENST00000504048
Hg19::chr4:53811852..53811859,+p1@ENST00000508813
Hg19::chr5:51986615..51986645,+p@chr5:51986615..51986645
+
Hg19::chr6:104674595..104674600,-p@chr6:104674595..104674600
-
Hg19::chr6:119812455..119812476,-p1@uc003pyn.1
Hg19::chr7:4051097..4051112,+p@chr7:4051097..4051112
+
Hg19::chr9:127267269..127267274,-p@chr9:127267269..127267274
-
Hg19::chr9:139553306..139553309,+p7@EGFL7
Hg19::chr9:35700153..35700160,-p@chr9:35700153..35700160
-


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:0048646anatomical structure formation0.00193832272984478
GO:0010324membrane invagination0.00193832272984478
GO:0006897endocytosis0.00193832272984478
GO:0016044membrane organization and biogenesis0.00431743742458901
GO:0009887organ morphogenesis0.00708308593722784
GO:0048645organ formation0.0117210525475664
GO:0042742defense response to bacterium0.0117210525475664
GO:0009617response to bacterium0.0117210525475664
GO:0002376immune system process0.0117210525475664
GO:0008289lipid binding0.0117210525475664
GO:0006952defense response0.0117210525475664
GO:0016188synaptic vesicle maturation0.0117210525475664
GO:0016192vesicle-mediated transport0.0117210525475664
GO:0001525angiogenesis0.0117210525475664
GO:0048514blood vessel morphogenesis0.0141790158821224
GO:0008368Gram-negative bacterial binding0.0143462514971166
GO:0001568blood vessel development0.0150345560599335
GO:0001944vasculature development0.0150345560599335
GO:0048536spleen development0.0153006412809464
GO:0004992platelet activating factor receptor activity0.0153006412809464
GO:0030128clathrin coat of endocytic vesicle0.0166289289310239
GO:0030669clathrin-coated endocytic vesicle membrane0.0166289289310239
GO:0030122AP-2 adaptor complex0.0166289289310239
GO:0051707response to other organism0.0170203211293769
GO:0030666endocytic vesicle membrane0.0170203211293769
GO:0048488synaptic vesicle endocytosis0.0170203211293769
GO:0007242intracellular signaling cascade0.0170203211293769
GO:0045334clathrin-coated endocytic vesicle0.0191182028028224
GO:0019932second-messenger-mediated signaling0.0239916635361042
GO:0009653anatomical structure morphogenesis0.0240215820592173
GO:0044459plasma membrane part0.0240215820592173
GO:0009607response to biotic stimulus0.0240215820592173
GO:0005041low-density lipoprotein receptor activity0.0240215820592173
GO:0030228lipoprotein receptor activity0.0240215820592173
GO:0008367bacterial binding0.0240215820592173
GO:0048513organ development0.0268474818617303
GO:0030132clathrin coat of coated pit0.0268474818617303
GO:0051704multi-organism process0.0280011431313333
GO:0006955immune response0.0284436603857437
GO:0016050vesicle organization and biogenesis0.0298074971666347
GO:0015035protein disulfide oxidoreductase activity0.0298074971666347
GO:0050435beta-amyloid metabolic process0.0301934221657316
GO:0030169low-density lipoprotein binding0.0301934221657316
GO:0048489synaptic vesicle transport0.0305445938335891
GO:0001570vasculogenesis0.0305445938335891
GO:0015036disulfide oxidoreductase activity0.034266593798573
GO:0030125clathrin vesicle coat0.034266593798573
GO:0030139endocytic vesicle0.034266593798573
GO:0016846carbon-sulfur lyase activity0.034266593798573
GO:0030665clathrin coated vesicle membrane0.0351030347467773
GO:0008034lipoprotein binding0.0433580422000358
GO:0005540hyaluronic acid binding0.0439847633389143
GO:0048731system development0.048251523533826
GO:0007165signal transduction0.0493670822384186



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><br>

Uber Anatomy
Ontology termp-valuen
spleen6.24e-883
gastrointestinal system mesentery6.24e-883
stomach region6.24e-883
mesentery6.24e-883
gastrointestinal system serosa6.24e-883
mesentery of stomach6.24e-883
gut mesentery6.24e-883
dorsal mesentery6.24e-883
dorsal mesogastrium6.24e-883
peritoneal cavity6.24e-883
spleen primordium6.24e-883
hemopoietic organ1.28e-847
immune organ1.28e-847
stomach6.50e-348
food storage organ6.50e-348
cavity lining4.59e-2312
serous membrane4.59e-2312
intraembryonic coelom4.59e-2312
mixed endoderm/mesoderm-derived structure1.88e-2129
thymus1.03e-174
hemolymphoid system gland1.03e-174
thymic region1.03e-174
pharyngeal gland1.03e-174
thymus primordium1.03e-174
viscus8.40e-1618
pharyngeal epithelium2.74e-126
gastrointestinal system2.63e-1125
neck6.56e-0810
gland of gut6.56e-0810
chordate pharynx6.56e-0810
pharyngeal region of foregut6.56e-0810
foregut7.10e-0887
immune system2.32e-0793
pharynx2.63e-0711
entire pharyngeal arch endoderm2.63e-0711
early pharyngeal endoderm2.63e-0711
hematopoietic system4.88e-0798
blood island4.88e-0798
body cavity7.30e-0746


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)
MA0003.17.37994e-05
MA0004.10.0287532
MA0006.10.0869544
MA0007.10.256778
MA0009.10.703091
MA0014.10.108527
MA0017.10.259054
MA0019.10.262257
MA0024.10.541347
MA0025.10.350278
MA0027.11.73105
MA0028.10.101617
MA0029.10.570205
MA0030.10.188804
MA0031.10.459469
MA0038.10.213125
MA0040.12.43965
MA0041.10.907724
MA0042.10.494507
MA0043.10.703596
MA0046.10.685727
MA0048.11.45411
MA0050.10.109642
MA0051.10.208758
MA0052.10.584895
MA0055.12.11283
MA0056.10
MA0057.12.50678
MA0058.10.153287
MA0059.10.151766
MA0060.10.103568
MA0061.11.16335
MA0063.10
MA0066.10.0588357
MA0067.10.49981
MA0068.11.56556
MA0069.10.242306
MA0070.11.23245
MA0071.12.02964
MA0072.10.231695
MA0073.11.71028e-06
MA0074.10.207985
MA0076.10.172646
MA0077.10.642781
MA0078.10.321356
MA0081.11.1143
MA0083.10.25765
MA0084.10.664025
MA0087.11.21472
MA0088.10.096627
MA0089.10
MA0090.11.69272
MA0091.10.850085
MA0092.10.718206
MA0093.10.00542575
MA0095.10
MA0098.10
MA0100.10.49318
MA0101.10.825635
MA0103.10.174928
MA0105.10.618389
MA0106.10.931456
MA0107.11.58248
MA0108.20.890829
MA0109.10
MA0111.10.983249
MA0113.10.0808928
MA0114.10.179021
MA0115.11.11194
MA0116.10.041195
MA0117.10.27892
MA0119.11.38212
MA0122.11.4653
MA0124.11.03875
MA0125.10.336564
MA0130.10
MA0131.10.10574
MA0132.10
MA0133.10
MA0135.10.27375
MA0136.10.0611972
MA0139.10.000203372
MA0140.10.172123
MA0141.11.88808
MA0142.10.133251
MA0143.10.582117
MA0144.10.841335
MA0145.10.277096
MA0146.10.0468954
MA0147.10.104091
MA0148.12.3103
MA0149.10.0422402
MA0062.20.210038
MA0035.20.688657
MA0039.20.152241
MA0138.20.322872
MA0002.20.589195
MA0137.20.107881
MA0104.20.0475142
MA0047.23.08253
MA0112.20.00931734
MA0065.20.292957
MA0150.10.360429
MA0151.10
MA0152.10.178362
MA0153.10.323801
MA0154.11.89362
MA0155.10.0028753
MA0156.10.110132
MA0157.11.24443
MA0158.10
MA0159.10.527617
MA0160.10.35201
MA0161.10
MA0162.15.33183e-05
MA0163.10.0050023
MA0164.11.02028
MA0080.20.555957
MA0018.20.0747401
MA0099.20.0472524
MA0079.20.317176
MA0102.20.697711
MA0258.10.24184
MA0259.10.0144768
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#2351254.913311854025770.003460565177026870.0175846818724035



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:C253&oldid=3067371"