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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.237220288771276,

Latest revision as of 11:21, 17 September 2013


Full id: C354_Fibroblast_Preadipocyte_Chondrocyte_chorionic_tenocyte_Synoviocyte_Smooth



Phase1 CAGE Peaks

Hg19::chr2:224840275..224840339,-p6@SERPINE2
Hg19::chr2:224840385..224840416,-p13@SERPINE2
Hg19::chr2:224840525..224840564,-p12@SERPINE2
Hg19::chr2:224840595..224840609,-p15@SERPINE2
Hg19::chr2:224840611..224840624,-p16@SERPINE2
Hg19::chr2:224842298..224842334,-p@chr2:224842298..224842334
-
Hg19::chr2:224845086..224845116,-p@chr2:224845086..224845116
-
Hg19::chr2:224847432..224847474,-p9@SERPINE2
Hg19::chr2:224849494..224849546,+p@chr2:224849494..224849546
+
Hg19::chr2:224849499..224849507,-p22@SERPINE2
Hg19::chr2:224849552..224849572,-p11@SERPINE2
Hg19::chr2:224849573..224849582,-p19@SERPINE2
Hg19::chr2:224849586..224849594,-p25@SERPINE2
Hg19::chr2:224849601..224849622,-p5@SERPINE2
Hg19::chr2:224849631..224849645,-p14@SERPINE2
Hg19::chr2:224849648..224849677,-p3@SERPINE2
Hg19::chr2:224856537..224856545,-p@chr2:224856537..224856545
-
Hg19::chr2:224856546..224856559,-p@chr2:224856546..224856559
-
Hg19::chr2:224856561..224856577,-p@chr2:224856561..224856577
-
Hg19::chr2:224856621..224856634,-p@chr2:224856621..224856634
-
Hg19::chr2:224856692..224856705,-p@chr2:224856692..224856705
-
Hg19::chr2:224856711..224856721,-p@chr2:224856711..224856721
-
Hg19::chr2:224862960..224863008,-p@chr2:224862960..224863008
-
Hg19::chr2:224862976..224862989,+p@chr2:224862976..224862989
+
Hg19::chr2:224863013..224863047,-p@chr2:224863013..224863047
-
Hg19::chr2:224866395..224866417,-p4@SERPINE2
Hg19::chr2:224866423..224866438,-p8@SERPINE2
Hg19::chr2:224866441..224866450,-p21@SERPINE2
Hg19::chr2:224866475..224866482,-p24@SERPINE2
Hg19::chr2:224866525..224866536,-p18@SERPINE2
Hg19::chr2:224866590..224866630,-p2@SERPINE2
Hg19::chr2:224903995..224904010,-p1@SERPINE2


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
fibroblast1.86e-1776
skin fibroblast1.00e-1123
Uber Anatomy
Ontology termp-valuen
skin of body1.15e-0941
integument1.79e-0846
integumental system1.79e-0846
organ component layer2.25e-0866
surface structure3.12e-0899
multilaminar epithelium2.69e-0783
omentum5.76e-076
peritoneum5.76e-076
abdominal cavity5.76e-076
visceral peritoneum5.76e-076


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)
MA0003.12.16634e-07
MA0004.10.288849
MA0006.10.0278021
MA0007.10.951942
MA0009.10.395891
MA0014.11.33333e-05
MA0017.10.350881
MA0019.12.18635
MA0024.10.312615
MA0025.10.508683
MA0027.11.93196
MA0028.10.032054
MA0029.10.327543
MA0030.12.34225
MA0031.10.270046
MA0038.10.429002
MA0040.10.332103
MA0041.10.645805
MA0042.10.0792314
MA0043.10.39615
MA0046.10.386991
MA0048.10.000662255
MA0050.10.273123
MA0051.10.136135
MA0052.10.335128
MA0055.18.43397e-05
MA0056.10
MA0057.10.100754
MA0058.10.177816
MA0059.10.0465255
MA0060.10.00694078
MA0061.10.0254374
MA0063.10
MA0066.13.4014
MA0067.10.673046
MA0068.10.00211477
MA0069.10.383853
MA0070.10.374777
MA0071.10.1171
MA0072.10.371146
MA0073.18.67895e-16
MA0074.11.3502
MA0076.10.0525452
MA0077.10.364942
MA0078.10.197204
MA0081.10.397764
MA0083.10.40206
MA0084.11.97407
MA0087.10.966048
MA0088.10.0321423
MA0089.10
MA0090.10.210825
MA0091.10.0865076
MA0092.10.525602
MA0093.10.118655
MA0095.10
MA0098.10
MA0100.10.146599
MA0101.10.029437
MA0103.10.263087
MA0105.10.00304723
MA0106.10.163029
MA0107.10.0137208
MA0108.20.267801
MA0109.10
MA0111.10.0631734
MA0113.10.173209
MA0114.10.0617658
MA0115.10.603788
MA0116.10.0672762
MA0117.10.427006
MA0119.10.0412526
MA0122.10.44876
MA0124.12.37995
MA0125.10.493194
MA0130.10
MA0131.10.2093
MA0132.10
MA0133.10
MA0135.11.07934
MA0136.10.142619
MA0139.10.00355142
MA0140.10.370231
MA0141.10.0459378
MA0142.10.247045
MA0143.12.24623
MA0144.10.0107485
MA0145.10.00552415
MA0146.10.000148203
MA0147.10.0696007
MA0148.11.09786
MA0149.10.110599
MA0062.20.004042
MA0035.20.744315
MA0039.29.14794e-08
MA0138.24.06714
MA0002.20.00577277
MA0137.20.0338658
MA0104.20.0365913
MA0047.20.155654
MA0112.20.0756164
MA0065.20.261847
MA0150.10.204231
MA0151.10
MA0152.12.45461
MA0153.11.20388
MA0154.10.37603
MA0155.10.000754999
MA0156.10.0345163
MA0157.10.227782
MA0158.10
MA0159.10.015016
MA0160.10.104733
MA0161.10
MA0162.10.00039512
MA0163.10.000379398
MA0164.10.181076
MA0080.20.0286016
MA0018.20.163878
MA0099.20.119388
MA0079.22.93116e-09
MA0102.20.88257
MA0258.10.00945121
MA0259.10.0164145
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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