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

Latest revision as of 11:26, 17 September 2013


Full id: C606_Endothelial_extraskeletal_Smooth_mesothelioma_Lymphatic_Fibroblast_lung



Phase1 CAGE Peaks

Hg19::chr4:145566841..145566862,+p10@HHIP
Hg19::chr4:145566874..145566889,+p15@HHIP
Hg19::chr4:145566965..145566978,-p2@ENST00000503066
Hg19::chr4:145567278..145567296,+p3@HHIP
Hg19::chr4:145567297..145567355,+p1@HHIP
Hg19::chr4:145567356..145567368,+p7@HHIP
Hg19::chr4:145567374..145567390,+p6@HHIP
Hg19::chr4:145567391..145567425,+p4@HHIP
Hg19::chr4:145567426..145567455,+p5@HHIP
Hg19::chr4:145567461..145567482,+p9@HHIP
Hg19::chr4:145567538..145567544,+p13@HHIP
Hg19::chr4:145567563..145567572,+p8@HHIP
Hg19::chr4:145608930..145608933,+p@chr4:145608930..145608933
+
Hg19::chr4:145629311..145629322,+p17@HHIP
Hg19::chr4:145662551..145662554,+p@chr4:145662551..145662554
+


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:0045879negative regulation of smoothened signaling pathway0.00156010832450253
GO:0040036regulation of fibroblast growth factor receptor signaling pathway0.0023401624867538
GO:0008589regulation of smoothened signaling pathway0.00364025275717257
GO:0007224smoothened signaling pathway0.00442030691942384
GO:0008543fibroblast growth factor receptor signaling pathway0.00442030691942384
GO:0007405neuroblast proliferation0.00442030691942384
GO:0009953dorsal/ventral pattern formation0.00624043329801013
GO:0030324lung development0.00745385088373431
GO:0030323respiratory tube development0.00745385088373431
GO:0003002regionalization0.013572942423172
GO:0009968negative regulation of signal transduction0.0147501150680239
GO:0035295tube development0.0148810332491011
GO:0007389pattern specification process0.0148810332491011
GO:0009986cell surface0.0164925737161696
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0218415165430354
GO:0048699generation of neurons0.0235966384081008
GO:0022008neurogenesis0.0240440224129214
GO:0007167enzyme linked receptor protein signaling pathway0.0260018054083755
GO:0009887organ morphogenesis0.0297241691299956



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
tube6.63e-45192
vessel3.19e-3968
vasculature2.34e-3878
vascular system2.34e-3878
anatomical conduit1.83e-36240
epithelial tube open at both ends6.32e-3659
blood vessel6.32e-3659
blood vasculature6.32e-3659
vascular cord6.32e-3659
splanchnic layer of lateral plate mesoderm4.14e-3283
cardiovascular system6.52e-32109
circulatory system2.08e-30112
artery3.02e-3042
arterial blood vessel3.02e-3042
arterial system3.02e-3042
cell layer4.94e-30309
epithelium3.80e-29306
epithelial tube1.34e-28117
anatomical cluster2.12e-27373
blood vessel endothelium4.59e-2318
endothelium4.59e-2318
cardiovascular system endothelium4.59e-2318
systemic artery8.99e-2333
systemic arterial system8.99e-2333
simple squamous epithelium1.56e-1722
squamous epithelium2.12e-1625
neural tube3.46e-1656
neural rod3.46e-1656
future spinal cord3.46e-1656
neural keel3.46e-1656
aorta1.77e-1421
aortic system1.77e-1421
regional part of nervous system2.66e-1453
regional part of brain2.66e-1453
structure with developmental contribution from neural crest5.81e-14132
neural plate9.41e-1482
presumptive neural plate9.41e-1482
neurectoderm2.40e-1386
endothelial tube1.17e-129
arterial system endothelium1.17e-129
endothelium of artery1.17e-129
unilaminar epithelium3.31e-12148
brain1.28e-1168
future brain1.28e-1168
multi-tissue structure2.66e-11342
regional part of forebrain1.66e-1041
forebrain1.66e-1041
anterior neural tube1.66e-1041
future forebrain1.66e-1041
telencephalon2.13e-1034
brain grey matter2.63e-1034
gray matter2.63e-1034
central nervous system3.25e-1081
pre-chordal neural plate1.46e-0961
nervous system2.13e-0989
regional part of telencephalon3.25e-0932
cerebral hemisphere4.40e-0932
ecto-epithelium9.45e-09104
germ layer1.15e-08560
germ layer / neural crest1.15e-08560
embryonic tissue1.15e-08560
presumptive structure1.15e-08560
germ layer / neural crest derived structure1.15e-08560
epiblast (generic)1.15e-08560
embryonic structure2.46e-08564
neural nucleus5.14e-089
nucleus of brain5.14e-089
developing anatomical structure5.14e-08581
umbilical blood vessel5.21e-089
anatomical system5.65e-08624
anatomical group6.78e-08625
adult organism7.91e-08114
lateral plate mesoderm9.11e-08203
embryo1.66e-07592
posterior neural tube2.85e-0715
chordal neural plate2.85e-0715
epithelial vesicle3.29e-0778
multi-cellular organism4.60e-07656
telencephalic nucleus9.00e-077


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)
MA0003.14.24829
MA0004.10.256222
MA0006.10.137644
MA0007.10.241375
MA0009.10.669377
MA0014.11.21411
MA0017.10.16476
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.148561
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.27117
MA0042.10.245557
MA0043.10.669676
MA0046.10.659066
MA0048.10.441458
MA0050.10.246257
MA0051.10.337676
MA0052.10.598036
MA0055.12.15314
MA0056.10
MA0057.11.83337
MA0058.10.182945
MA0059.10.182001
MA0060.10.0671843
MA0061.12.76473
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.10.147451
MA0069.10.655419
MA0070.10.644843
MA0071.10.308534
MA0072.10.640598
MA0073.10.000193423
MA0074.10.894848
MA0076.10.194691
MA0077.10.633326
MA0078.10.424186
MA0081.10.18212
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.426561
MA0089.10
MA0090.10.205547
MA0091.12.03783
MA0092.10.228476
MA0093.10.139688
MA0095.10
MA0098.10
MA0100.10.353174
MA0101.10.141917
MA0103.10.131472
MA0105.15.00275
MA0106.10.37688
MA0107.10.315431
MA0108.20.515791
MA0109.10
MA0111.10.215855
MA0113.10.39123
MA0114.10.0920489
MA0115.10.900969
MA0116.12.86257
MA0117.10.705104
MA0119.10.508209
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.11.96188
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.406749
MA0140.10.30631
MA0141.10.180729
MA0142.10.489543
MA0143.10.391385
MA0144.10.0838502
MA0145.10.135956
MA0146.10.197185
MA0147.10.0991954
MA0148.10.276339
MA0149.10.298252
MA0062.20.0512998
MA0035.20.305721
MA0039.21.29697
MA0138.20.425279
MA0002.20.480166
MA0137.20.153033
MA0104.20.236755
MA0047.20.366327
MA0112.20.0445156
MA0065.20.287056
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.10.0156321
MA0155.10.6552
MA0156.10.154615
MA0157.10.46471
MA0158.10
MA0159.10.671959
MA0160.10.288813
MA0161.10
MA0162.12.73267
MA0163.10.563152
MA0164.10.402162
MA0080.20.139746
MA0018.25.76696
MA0099.20.312108
MA0079.213.695
MA0102.21.1957
MA0258.10.0785319
MA0259.10.104286
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#1879105.937644564379345.57766636877494e-072.57868923368077e-05
FOS#2353105.998636872596275.06473487999527e-072.36987386259778e-05



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.

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