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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.47689857423244,

Latest revision as of 11:28, 17 September 2013


Full id: C666_tenocyte_Synoviocyte_Fibroblast_Chondrocyte_Nucleus_normal_mesenchymal



Phase1 CAGE Peaks

Hg19::chr1:56962127..56962135,-p@chr1:56962127..56962135
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Hg19::chr1:56962213..56962224,-p@chr1:56962213..56962224
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Hg19::chr1:56977768..56977801,-p@chr1:56977768..56977801
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Hg19::chr1:56977818..56977827,-p@chr1:56977818..56977827
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Hg19::chr1:56990054..56990076,-p@chr1:56990054..56990076
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Hg19::chr1:56990149..56990181,-p@chr1:56990149..56990181
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Hg19::chr1:56990206..56990220,-p@chr1:56990206..56990220
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Hg19::chr1:57044697..57044720,-p9@PPAP2B
Hg19::chr1:57044945..57044953,-p13@PPAP2B
Hg19::chr1:57044980..57045112,-p1@PPAP2B
Hg19::chr1:57045115..57045143,-p6@PPAP2B
Hg19::chr1:57045207..57045226,-p2@PPAP2B
Hg19::chr1:57045228..57045242,-p3@PPAP2B


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>

Cell Type
Ontology termp-valuen
fibroblast2.40e-1176
skin fibroblast3.83e-1023
fat cell3.89e-0815
Uber Anatomy
Ontology termp-valuen
adult organism6.89e-22114
multi-cellular organism4.14e-11656
structure with developmental contribution from neural crest1.37e-10132
neural tube2.44e-1056
neural rod2.44e-1056
future spinal cord2.44e-1056
neural keel2.44e-1056
brain grey matter2.81e-0934
gray matter2.81e-0934
regional part of nervous system3.65e-0953
regional part of brain3.65e-0953
telencephalon4.60e-0934
central nervous system1.12e-0881
regional part of telencephalon1.27e-0832
cerebral hemisphere1.28e-0832
surface structure2.22e-0899
organ2.43e-08503
regional part of forebrain8.61e-0841
forebrain8.61e-0841
anterior neural tube8.61e-0841
future forebrain8.61e-0841
anatomical system9.04e-08624
neural plate9.21e-0882
presumptive neural plate9.21e-0882
anatomical group1.15e-07625
integument1.25e-0746
integumental system1.25e-0746
multi-tissue structure1.93e-07342
brain2.60e-0768
future brain2.60e-0768
skin of body2.97e-0741
neurectoderm8.05e-0786


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)
MA0003.10.00135586
MA0004.10.297884
MA0006.10.169524
MA0007.10.282081
MA0009.10.724811
MA0014.10.129679
MA0017.10.199401
MA0019.10.428118
MA0024.10.6245
MA0025.10.854131
MA0027.12.32165
MA0028.10.181601
MA0029.10.642879
MA0030.10.63197
MA0031.10.570886
MA0038.10.387473
MA0040.10.648455
MA0041.10.313738
MA0042.10.781261
MA0043.10.725115
MA0046.10.714324
MA0048.11.28679
MA0050.10.287284
MA0051.10.383704
MA0052.10.652145
MA0055.114.7567
MA0056.10
MA0057.10.0301256
MA0058.10.219229
MA0059.10.218203
MA0060.10.0892161
MA0061.10.0732084
MA0063.10
MA0066.10.387854
MA0067.11.03434
MA0068.11.16318
MA0069.10.710614
MA0070.10.69985
MA0071.10.35315
MA0072.10.695528
MA0073.15.08229e-05
MA0074.10.383033
MA0076.10.655479
MA0077.10.688123
MA0078.10.473657
MA0081.10.623454
MA0083.10.732051
MA0084.11.21913
MA0087.10.693179
MA0088.10.170244
MA0089.10
MA0090.11.96147
MA0091.10.30011
MA0092.10.739628
MA0093.10.171791
MA0095.10
MA0098.10
MA0100.10.399896
MA0101.10.17426
MA0103.10.489275
MA0105.10.0255214
MA0106.10.424592
MA0107.10.121572
MA0108.20.568002
MA0109.10
MA0111.10.254772
MA0113.10.439505
MA0114.10.118142
MA0115.10.959312
MA0116.11.85415
MA0117.10.76111
MA0119.10.593096
MA0122.10.786181
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.10.490408
MA0132.10
MA0133.10
MA0135.10.754112
MA0136.10.393782
MA0139.10.50732
MA0140.10.350813
MA0141.10.216821
MA0142.10.541045
MA0143.10.439666
MA0144.10.108694
MA0145.10.0164225
MA0146.10.000600379
MA0147.10.126316
MA0148.10.319209
MA0149.10.342334
MA0062.20.0702147
MA0035.20.350194
MA0039.20.00196561
MA0138.20.474787
MA0002.20.0821804
MA0137.20.186529
MA0104.20.088751
MA0047.20.413608
MA0112.20.0689988
MA0065.20.0171659
MA0150.10.238884
MA0151.10
MA0152.10.356591
MA0153.10.820317
MA0154.10.0246626
MA0155.10.167839
MA0156.10.18827
MA0157.10.515488
MA0158.10
MA0159.10.126752
MA0160.11.58936
MA0161.10
MA0162.10.00205586
MA0163.10.000991488
MA0164.10.450848
MA0080.20.171855
MA0018.20.425847
MA0099.20.356906
MA0079.20.201216
MA0102.21.25596
MA0258.10.102521
MA0259.10.412624
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
REST#597864.45385940744370.001112236766968470.00772141024364667
SMC3#912655.786512632666480.001060752950196980.00749502586872485
TAF7#687965.276801263811040.0004462923201972710.00415384757410951
TCF7L2#693454.142375601206670.004688503444004930.022119646347221
ZNF263#1012763.794696140158770.002585173580546710.0142989589862683



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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