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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.206356141027287,

Latest revision as of 11:26, 17 September 2013


Full id: C581_Fibroblast_Keratocytes_Lens_CD14_Mesenchymal_Hepatic_Hair



Phase1 CAGE Peaks

Hg19::chr10:17271266..17271286,+p1@VIM
Hg19::chr10:17271909..17272033,-p1@uc001iot.1
Hg19::chr10:17272625..17272692,+p@chr10:17272625..17272692
+
Hg19::chr10:17275575..17275660,+p3@VIM
Hg19::chr10:17275758..17275914,+p@chr10:17275758..17275914
+
Hg19::chr10:17276681..17276732,+p@chr10:17276681..17276732
+
Hg19::chr10:17276737..17276787,+p@chr10:17276737..17276787
+
Hg19::chr10:17277164..17277180,+p@chr10:17277164..17277180
+
Hg19::chr10:17277196..17277231,+p@chr10:17277196..17277231
+
Hg19::chr10:17277273..17277306,+p@chr10:17277273..17277306
+
Hg19::chr10:17277329..17277340,+p@chr10:17277329..17277340
+
Hg19::chr10:17277832..17277867,+p@chr10:17277832..17277867
+
Hg19::chr10:17278284..17278356,+p4@VIM
Hg19::chr10:17279217..17279304,+p@chr10:17279217..17279304
+
Hg19::chr6:126923668..126923692,-p@chr6:126923668..126923692
-


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:0045103intermediate filament-based process0.0101554221123278
GO:0005200structural constituent of cytoskeleton0.0287736959849288
GO:0045111intermediate filament cytoskeleton0.0399446603084893
GO:0005882intermediate filament0.0399446603084893
GO:0051674localization of cell0.0432169629891283
GO:0006928cell motility0.0432169629891283



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>

Cell Type
Ontology termp-valuen
somatic cell1.61e-28588
multi fate stem cell1.05e-25427
somatic stem cell7.50e-24433
stem cell1.58e-22441
fibroblast8.21e-1876
mesodermal cell4.73e-16121
defensive cell6.80e-1648
phagocyte6.80e-1648
classical monocyte2.00e-1442
CD14-positive, CD16-negative classical monocyte2.00e-1442
connective tissue cell9.77e-14361
stuff accumulating cell1.37e-1387
macrophage dendritic cell progenitor1.38e-1361
animal cell1.89e-13679
eukaryotic cell1.89e-13679
granulocyte monocyte progenitor cell3.64e-1367
monopoietic cell3.94e-1359
monocyte3.94e-1359
monoblast3.94e-1359
promonocyte3.94e-1359
non-terminally differentiated cell5.67e-13106
muscle precursor cell1.05e-1258
myoblast1.05e-1258
multi-potent skeletal muscle stem cell1.05e-1258
mesenchymal cell2.49e-12354
muscle cell5.34e-1255
motile cell5.57e-12386
contractile cell6.45e-1259
myeloid lineage restricted progenitor cell9.39e-1266
myeloid leukocyte2.85e-1172
electrically responsive cell6.93e-1161
electrically active cell6.93e-1161
smooth muscle cell2.54e-1043
smooth muscle myoblast2.54e-1043
skin fibroblast5.41e-0923
vascular associated smooth muscle cell7.97e-0932
native cell1.85e-08722
Uber Anatomy
Ontology termp-valuen
musculoskeletal system2.27e-29167
mesoderm3.52e-29315
mesoderm-derived structure3.52e-29315
presumptive mesoderm3.52e-29315
lateral plate mesoderm3.79e-24203
vasculature3.74e-1678
vascular system3.74e-1678
skeletal system1.02e-15100
epithelial vesicle1.30e-1578
somite1.48e-1571
presomitic mesoderm1.48e-1571
presumptive segmental plate1.48e-1571
dermomyotome1.48e-1571
trunk paraxial mesoderm1.48e-1571
dense mesenchyme tissue1.50e-1573
paraxial mesoderm5.10e-1572
presumptive paraxial mesoderm5.10e-1572
cardiovascular system5.33e-15109
vessel1.31e-1468
bone marrow4.42e-1476
connective tissue4.76e-14371
circulatory system4.92e-14112
skeletal element5.73e-1490
epithelial tube open at both ends1.47e-1359
blood vessel1.47e-1359
blood vasculature1.47e-1359
vascular cord1.47e-1359
splanchnic layer of lateral plate mesoderm1.77e-1383
bone element5.09e-1382
artery5.68e-1342
arterial blood vessel5.68e-1342
arterial system5.68e-1342
multilaminar epithelium1.49e-1283
immune system3.27e-1293
skeletal muscle tissue4.39e-1262
striated muscle tissue4.39e-1262
myotome4.39e-1262
muscle tissue2.41e-1164
musculature2.41e-1164
musculature of body2.41e-1164
systemic artery2.64e-1033
systemic arterial system2.64e-1033
hemolymphoid system6.60e-10108
hematopoietic system5.01e-0998
blood island5.01e-0998
integument8.07e-0846
integumental system8.07e-0846
aorta9.60e-0821
aortic system9.60e-0821
unilaminar epithelium8.93e-07148


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)
MA0003.10.0558959
MA0004.10.256222
MA0006.10.426713
MA0007.11.94933
MA0009.10.669377
MA0014.10.0115261
MA0017.10.494446
MA0019.10.990457
MA0024.12.39368
MA0025.10.796882
MA0027.12.25966
MA0028.10.148561
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.746198
MA0042.11.27338
MA0043.10.669676
MA0046.10.659066
MA0048.11.0552
MA0050.10.246257
MA0051.10.337676
MA0052.11.45703
MA0055.10.120131
MA0056.10
MA0057.10.0873069
MA0058.10.182945
MA0059.10.182001
MA0060.10.237888
MA0061.10.43901
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.10.964815
MA0069.10.655419
MA0070.10.644843
MA0071.12.29218
MA0072.10.640598
MA0073.10.608608
MA0074.10.337035
MA0076.10.194691
MA0077.10.633326
MA0078.10.424186
MA0081.10.18212
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.0411204
MA0089.10
MA0090.10.205547
MA0091.11.32108
MA0092.11.2087
MA0093.10.139688
MA0095.10
MA0098.10
MA0100.10.930697
MA0101.10.437519
MA0103.10.411001
MA0105.10.623178
MA0106.10.37688
MA0107.10.650533
MA0108.20.515791
MA0109.10
MA0111.10.215855
MA0113.11.01449
MA0114.10.30732
MA0115.10.900969
MA0116.10.320986
MA0117.10.705104
MA0119.10.170362
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.406749
MA0140.10.30631
MA0141.11.61764
MA0142.10.489543
MA0143.10.391385
MA0144.10.0838502
MA0145.10.135956
MA0146.10.0082386
MA0147.10.0991954
MA0148.10.276339
MA0149.10.298252
MA0062.20.0512998
MA0035.20.824687
MA0039.20.122601
MA0138.20.425279
MA0002.20.0612545
MA0137.22.09053
MA0104.20.0667907
MA0047.20.959769
MA0112.20.0445156
MA0065.20.0514203
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.10.187751
MA0155.10.0403226
MA0156.10.154615
MA0157.10.46471
MA0158.10
MA0159.10.0995776
MA0160.10.288813
MA0161.10
MA0162.10.0634394
MA0163.10.0128736
MA0164.10.402162
MA0080.20.139746
MA0018.20.378086
MA0099.20.312108
MA0079.20.00055716
MA0102.21.1957
MA0258.10.0785319
MA0259.10.340204
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
CTCF#10664103.573504248716686.07197623972401e-050.000996309703850017
MAFK#797559.033577712609970.0001503357337649870.00193694962974111
POLR2A#5430131.861126086350330.001642058826741280.010274082303261
RAD21#588553.451677965152110.01100947940992650.0405008460758478
ZBTB33#10009510.55490834332717.22167785884653e-050.00113570970320746



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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