Personal tools

Coexpression cluster:C357: 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 11:21, 17 September 2013


Full id: C357_Endothelial_Lymphatic_Renal_Hepatic_seminal_breast_heart



Phase1 CAGE Peaks

Hg19::chr10:45477877..45477901,+p2@RASSF4
Hg19::chr14:51863894..51863903,-p1@ENST00000556762
Hg19::chr15:65398647..65398656,-p3@UBAP1L
Hg19::chr15:65935213..65935234,+p8@SLC24A1
Hg19::chr15:65935239..65935275,+p6@SLC24A1
Hg19::chr15:65935283..65935297,+p11@SLC24A1
Hg19::chr18:54339814..54339822,+p7@WDR7
Hg19::chr18:54339823..54339834,+p8@WDR7
Hg19::chr19:42006553..42006555,-p1@LOC100505495
Hg19::chr19:4639579..4639589,+p2@TNFAIP8L1
Hg19::chr1:1148395..1148419,-p@chr1:1148395..1148419
-
Hg19::chr1:214453986..214454002,+p10@SMYD2
Hg19::chr1:94526344..94526353,-p4@ABCA4
Hg19::chr1:94526365..94526386,-p2@ABCA4
Hg19::chr20:62679771..62679782,-p4@SOX18
Hg19::chr22:43042678..43042692,-p3@CYB5R3
Hg19::chr2:127413798..127413819,+p3@GYPC
Hg19::chr2:33661536..33661549,+p17@RASGRP3
Hg19::chr2:71681572..71681579,-p@chr2:71681572..71681579
-
Hg19::chr3:194868625..194868636,+p2@ENST00000426468
Hg19::chr3:194868639..194868654,+p1@ENST00000426468
Hg19::chr3:30560333..30560348,+p@chr3:30560333..30560348
+
Hg19::chr3:30560368..30560379,+p@chr3:30560368..30560379
+
Hg19::chr4:146403815..146403832,-p1@BC035666
Hg19::chr4:146403984..146404001,-p1@AK023324
Hg19::chr4:146404016..146404030,-p2@AK023324
Hg19::chr4:189881560..189881604,-p@chr4:189881560..189881604
-
Hg19::chr6:168195926..168195943,+p1@LOC441179
Hg19::chr6:168195978..168195989,+p3@LOC441179
Hg19::chr8:21924052..21924103,+p6@EPB49
Hg19::chrX:107068687..107068703,+p6@MID2


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

p.valueFDRnGenesnPathwayName
2.5936681633843e-050.0082089597371113217{CNGB1,17} (Static Module):NA
1.73680731938346e-050.0082089597371113214{HMGB1,14} (Static Module):NA



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:0009416response to light stimulus0.025522668176794
GO:0006649phospholipid transfer to membrane0.025522668176794
GO:0009642response to light intensity0.025522668176794
GO:0019867outer membrane0.025522668176794
GO:0009314response to radiation0.025522668176794
GO:0005887integral to plasma membrane0.025522668176794
GO:0031226intrinsic to plasma membrane0.025522668176794
GO:0008273calcium, potassium:sodium antiporter activity0.0297804699504777
GO:0046582Rap GTPase activator activity0.0297804699504777
GO:0009628response to abiotic stimulus0.0324830039881413
GO:0007603phototransduction, visible light0.0324830039881413
GO:0004128cytochrome-b5 reductase activity0.0417498825370661
GO:0016653oxidoreductase activity, acting on NADH or NADPH, heme protein as acceptor0.0417498825370661
GO:0007601visual perception0.0417498825370661
GO:0050953sensory perception of light stimulus0.0417498825370661
GO:0015674di-, tri-valent inorganic cation transport0.0478365347063914



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>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
blood vessel endothelium3.20e-3918
endothelium3.20e-3918
cardiovascular system endothelium3.20e-3918
simple squamous epithelium1.89e-3122
squamous epithelium2.97e-2725
endothelial tube2.11e-209
arterial system endothelium2.11e-209
endothelium of artery2.11e-209
vessel7.16e-2068
lymphoid system3.94e-1810
lymphatic vessel2.16e-178
lymph vasculature2.16e-178
lymphatic part of lymphoid system2.16e-178
vasculature1.26e-1678
vascular system1.26e-1678
microcirculatory vessel5.99e-133
endothelium of capillary5.99e-133
capillary5.99e-133
cardiovascular system1.33e-11109
epithelial tube open at both ends3.78e-1159
blood vessel3.78e-1159
blood vasculature3.78e-1159
vascular cord3.78e-1159
circulatory system3.80e-11112
anatomical cluster1.69e-10373
splanchnic layer of lateral plate mesoderm2.05e-1083
vein3.21e-109
venous blood vessel3.21e-109
venous system3.21e-109
adult organism2.44e-09114
epithelial tube4.01e-09117
anatomical conduit5.01e-09240
segment of aorta6.50e-092
thoracic aorta6.50e-092
open tracheal system trachea4.04e-082
mesonephric epithelium1.14e-078
mesonephric tubule1.14e-078
nephric duct1.14e-078
renal duct1.14e-078
mesonephric duct1.14e-078
pronephric duct1.14e-078
intraembryonic coelom1.58e-0712
umbilical vein3.19e-075
mesonephros8.14e-079
pronephros8.14e-079
nephrogenic cord8.14e-079
pronephric mesoderm8.14e-079
rostral part of nephrogenic cord8.14e-079
presumptive pronephric mesoderm8.14e-079


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)
MA0003.10.0188063
MA0004.10.629016
MA0006.10.124841
MA0007.10.0818413
MA0009.10.406485
MA0014.10.0345374
MA0017.10.0420572
MA0019.10.172846
MA0024.10.322368
MA0025.10.520106
MA0027.11.94566
MA0028.10.0349277
MA0029.10.337465
MA0030.10.875776
MA0031.10.279263
MA0038.10.145356
MA0040.11.62355
MA0041.10.672034
MA0042.10.59843
MA0043.10.406746
MA0046.10.397506
MA0048.10.124274
MA0050.10.0846723
MA0051.10.142882
MA0052.10.912859
MA0055.10.2042
MA0056.10
MA0057.10.20555
MA0058.10.421253
MA0059.10.187652
MA0060.10.116876
MA0061.10.0861879
MA0063.10
MA0066.10.145606
MA0067.10.685278
MA0068.10.821915
MA0069.10.394339
MA0070.10.385179
MA0071.10.123343
MA0072.10.381514
MA0073.10.000812926
MA0074.10.863251
MA0076.10.0564857
MA0077.12.61585
MA0078.11.11907
MA0081.11.13049
MA0083.10.412707
MA0084.10.860109
MA0087.10.379524
MA0088.10.0379179
MA0089.10
MA0090.10.836434
MA0091.10.306639
MA0092.11.39879
MA0093.10.302394
MA0095.10
MA0098.10
MA0100.11.45929
MA0101.10.89179
MA0103.10.519443
MA0105.10.169529
MA0106.10.170405
MA0107.10.904088
MA0108.20.759502
MA0109.10
MA0111.10.239028
MA0113.10.180801
MA0114.10.177592
MA0115.10.615724
MA0116.10.0735945
MA0117.10.437859
MA0119.11.50307
MA0122.11.16324
MA0124.10.578498
MA0125.10.50452
MA0130.10
MA0131.10.217579
MA0132.10
MA0133.10
MA0135.10.431776
MA0136.11.4348
MA0139.10.0738384
MA0140.10.386354
MA0141.10.185774
MA0142.10.255934
MA0143.10.533941
MA0144.10.0585629
MA0145.10.278532
MA0146.10.393109
MA0147.10.0760571
MA0148.10.102785
MA0149.11.79212
MA0062.20.51839
MA0035.20.121502
MA0039.20.00265764
MA0138.20.20609
MA0002.20.219603
MA0137.20.0368453
MA0104.20.00782014
MA0047.20.489777
MA0112.20.250412
MA0065.20.0529546
MA0150.10.472127
MA0151.10
MA0152.10.395672
MA0153.10.489927
MA0154.10.0393943
MA0155.10.138174
MA0156.11.38249
MA0157.10.665783
MA0158.10
MA0159.10.196704
MA0160.10.110614
MA0161.10
MA0162.10.0869856
MA0163.10.039767
MA0164.10.188828
MA0080.20.554955
MA0018.20.171273
MA0099.20.125694
MA0079.20.00155208
MA0102.20.895427
MA0258.10.144068
MA0259.10.40277
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

This analysis result is provided for C0 - C305 clusters.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C357&oldid=3067474"