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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.237220288771276

Latest revision as of 11:25, 17 September 2013


Full id: C547_Renal_Endothelial_Mesenchymal_Hepatic_Smooth_Fibroblast_Alveolar



Phase1 CAGE Peaks

Hg19::chr1:22163333..22163340,-p6@HSPG2
Hg19::chr1:22181125..22181132,-p15@HSPG2
Hg19::chr1:22186101..22186129,-p@chr1:22186101..22186129
-
Hg19::chr1:22203039..22203053,-p@chr1:22203039..22203053
-
Hg19::chr1:22203092..22203119,-p@chr1:22203092..22203119
-
Hg19::chr1:22204962..22204969,-p4@HSPG2
Hg19::chr1:22206973..22206987,-p@chr1:22206973..22206987
-
Hg19::chr1:22207217..22207234,-p@chr1:22207217..22207234
-
Hg19::chr1:22211127..22211133,+p@chr1:22211127..22211133
+
Hg19::chr1:22211913..22211920,+p@chr1:22211913..22211920
+
Hg19::chr1:22213979..22214020,-p@chr1:22213979..22214020
-
Hg19::chr1:22214092..22214113,+p@chr1:22214092..22214113
+
Hg19::chr1:22214103..22214127,-p@chr1:22214103..22214127
-
Hg19::chr1:22214518..22214534,-p@chr1:22214518..22214534
-
Hg19::chr1:22216505..22216565,-p@chr1:22216505..22216565
-
Hg19::chr1:22222766..22222805,-p2@HSPG2
Hg19::chr1:22263793..22263811,-p1@HSPG2


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

No GOStat results

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
splanchnic layer of lateral plate mesoderm2.65e-2783
vessel6.57e-2668
epithelial tube1.96e-24117
epithelial tube open at both ends1.71e-2259
blood vessel1.71e-2259
blood vasculature1.71e-2259
vascular cord1.71e-2259
vasculature7.62e-2278
vascular system7.62e-2278
circulatory system1.22e-19112
cardiovascular system9.41e-19109
artery6.74e-1542
arterial blood vessel6.74e-1542
arterial system6.74e-1542
blood vessel endothelium2.08e-1418
endothelium2.08e-1418
cardiovascular system endothelium2.08e-1418
squamous epithelium3.84e-1425
simple squamous epithelium9.19e-1422
anatomical conduit6.48e-12240
mesoderm9.29e-12315
mesoderm-derived structure9.29e-12315
presumptive mesoderm9.29e-12315
unilaminar epithelium7.04e-11148
systemic artery9.38e-1133
systemic arterial system9.38e-1133
trunk mesenchyme4.84e-10122
mesenchyme3.14e-09160
entire embryonic mesenchyme3.14e-09160
multi-cellular organism4.07e-09656
trunk1.05e-08199
primary circulatory organ1.26e-0827
endothelial tube3.14e-089
arterial system endothelium3.14e-089
endothelium of artery3.14e-089
intermediate mesoderm3.24e-0828
urogenital ridge3.63e-0811
aorta4.25e-0821
aortic system4.25e-0821
epithelial vesicle6.24e-0878
heart8.66e-0824
primitive heart tube8.66e-0824
primary heart field8.66e-0824
anterior lateral plate mesoderm8.66e-0824
heart tube8.66e-0824
heart primordium8.66e-0824
cardiac mesoderm8.66e-0824
cardiogenic plate8.66e-0824
heart rudiment8.66e-0824
compound organ1.59e-0768
organism subdivision1.69e-07264
muscle tissue2.22e-0764
musculature2.22e-0764
musculature of body2.22e-0764
skeletal muscle tissue5.80e-0762
striated muscle tissue5.80e-0762
myotome5.80e-0762
tube6.95e-07192
mesonephros7.15e-079
pronephros7.15e-079
nephrogenic cord7.15e-079
pronephric mesoderm7.15e-079
rostral part of nephrogenic cord7.15e-079
presumptive pronephric mesoderm7.15e-079
epithelium9.60e-07306


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)
MA0003.10.805327
MA0004.10.221943
MA0006.10.112549
MA0007.12.4995
MA0009.10.621697
MA0014.10.086513
MA0017.10.840365
MA0019.10.901513
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.10.387666
MA0029.10.542771
MA0030.10.532314
MA0031.10.474026
MA0038.10.302644
MA0040.10.548121
MA0041.10.236024
MA0042.10.211928
MA0043.10.621991
MA0046.10.611559
MA0048.10.345177
MA0050.10.212584
MA0051.10.299199
MA0052.10.551663
MA0055.10.429976
MA0056.10
MA0057.10.164004
MA0058.10.153757
MA0059.10.15289
MA0060.10.0509127
MA0061.10.356644
MA0063.10
MA0066.10.818531
MA0067.10.924196
MA0068.10.111262
MA0069.10.607975
MA0070.10.597583
MA0071.10.27142
MA0072.10.593415
MA0073.11.99415
MA0074.11.46857
MA0076.10.164578
MA0077.10.586275
MA0078.10.382364
MA0081.10.465308
MA0083.10.628701
MA0084.11.10674
MA0087.10.591148
MA0088.10.514158
MA0089.10
MA0090.10.518617
MA0091.10.223914
MA0092.10.195947
MA0093.10.366841
MA0095.10
MA0098.10
MA0100.10.314026
MA0101.10.116395
MA0103.11.16516
MA0105.10.14145
MA0106.10.894258
MA0107.10.259598
MA0108.20.471286
MA0109.10
MA0111.11.03566
MA0113.12.49772
MA0114.10.537797
MA0115.10.850405
MA0116.10.949722
MA0117.11.58019
MA0119.10.438293
MA0122.10.681203
MA0124.10.810546
MA0125.10.730403
MA0130.10
MA0131.11.02939
MA0132.10
MA0133.10
MA0135.10.650071
MA0136.10.30842
MA0139.10.0351037
MA0140.10.269307
MA0141.10.462123
MA0142.10.445733
MA0143.10.925263
MA0144.10.231909
MA0145.10.838342
MA0146.11.2525
MA0147.10.569428
MA0148.10.240905
MA0149.10.261654
MA0062.20.148712
MA0035.20.740647
MA0039.20.593425
MA0138.20.38342
MA0002.20.174654
MA0137.20.126444
MA0104.20.188874
MA0047.20.326636
MA0112.21.79957
MA0065.21.52581
MA0150.10.170499
MA0151.10
MA0152.10.274535
MA0153.10.714423
MA0154.13.2396
MA0155.14.05081
MA0156.10.12788
MA0157.10.421609
MA0158.10
MA0159.10.270712
MA0160.10.252705
MA0161.10
MA0162.11.00547
MA0163.13.62767
MA0164.10.361105
MA0080.20.366978
MA0018.20.337929
MA0099.20.27482
MA0079.20.0845756
MA0102.21.14323
MA0258.10.476351
MA0259.10.28219
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.

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