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Coexpression cluster:C568: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=1.03941737036424

Latest revision as of 11:25, 17 September 2013


Full id: C568_Mesenchymal_Fibroblast_Adipocyte_Preadipocyte_Chondrocyte_aorta_Smooth



Phase1 CAGE Peaks

Hg19::chr15:89441939..89441998,-p@chr15:89441939..89441998
-
Hg19::chr15:89442320..89442341,-p@chr15:89442320..89442341
-
Hg19::chr15:89442416..89442454,-p@chr15:89442416..89442454
-
Hg19::chr15:89442478..89442529,-p@chr15:89442478..89442529
-
Hg19::chr15:89442594..89442640,-p@chr15:89442594..89442640
-
Hg19::chr15:89442654..89442681,-p@chr15:89442654..89442681
-
Hg19::chr15:89442979..89443002,-p@chr15:89442979..89443002
-
Hg19::chr15:89443005..89443024,-p@chr15:89443005..89443024
-
Hg19::chr15:89444827..89444838,-p10@MFGE8
Hg19::chr15:89444877..89444891,-p6@MFGE8
Hg19::chr15:89444904..89444930,+p@chr15:89444904..89444930
+
Hg19::chr15:89444937..89444980,-p5@MFGE8
Hg19::chr15:89449904..89449998,-p4@MFGE8
Hg19::chr15:89450494..89450525,-p@chr15:89450494..89450525
-
Hg19::chr15:89453066..89453095,-p7@MFGE8
Hg19::chr15:89456602..89456618,-p1@MFGE8


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
fibroblast4.45e-1476
non-terminally differentiated cell7.78e-10106
stromal cell2.17e-0828
preadipocyte3.73e-0712
pigment cell6.79e-0714
Uber Anatomy
Ontology termp-valuen
surface structure6.79e-1199
reproductive structure1.76e-1059
reproductive system1.76e-1059
reproductive organ1.04e-0748
integument1.88e-0746
integumental system1.88e-0746
organ component layer4.83e-0766


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)
MA0003.10.176373
MA0004.10.238283
MA0006.10.124371
MA0007.10.223897
MA0009.10.644692
MA0014.10.024058
MA0017.10.150184
MA0019.10.944302
MA0024.10.547222
MA0025.10.771296
MA0027.12.23171
MA0028.10.419336
MA0029.10.565022
MA0030.10.554453
MA0031.10.495474
MA0038.10.321141
MA0040.10.570428
MA0041.10.252793
MA0042.10.227947
MA0043.10.644989
MA0046.10.634468
MA0048.10.390294
MA0050.10.228625
MA0051.10.317617
MA0052.10.574006
MA0055.10.0967754
MA0056.10
MA0057.10.615711
MA0058.10.167587
MA0059.10.166682
MA0060.10.0584466
MA0061.10.0461955
MA0063.10
MA0066.10.321498
MA0067.10.948938
MA0068.10.880335
MA0069.11.52585
MA0070.10.620368
MA0071.10.289163
MA0072.10.616162
MA0073.10.47148
MA0074.10.316991
MA0076.10.178863
MA0077.10.608956
MA0078.10.402443
MA0081.10.166796
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.10.369952
MA0089.10
MA0090.10.554239
MA0091.10.240316
MA0092.10.607109
MA0093.10.12631
MA0095.10
MA0098.10
MA0100.10.332778
MA0101.10.128426
MA0103.12.44742
MA0105.10.0621554
MA0106.10.93695
MA0107.10.0842574
MA0108.20.492699
MA0109.10
MA0111.10.578093
MA0113.10.370073
MA0114.10.278245
MA0115.10.874839
MA0116.10.607827
MA0117.10.680135
MA0119.15.31185
MA0122.10.70466
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.10.418384
MA0132.10
MA0133.10
MA0135.10.673296
MA0136.10.327047
MA0139.10.159457
MA0140.10.286995
MA0141.10.165463
MA0142.10.4668
MA0143.10.370225
MA0144.10.0738381
MA0145.10.418252
MA0146.10.155412
MA0147.10.296651
MA0148.10.257816
MA0149.12.14464
MA0062.20.168482
MA0035.20.780994
MA0039.20.217508
MA0138.20.403517
MA0002.20.434729
MA0137.20.138998
MA0104.20.211351
MA0047.20.345656
MA0112.21.20168
MA0065.20.667633
MA0150.10.185024
MA0151.10
MA0152.10.292357
MA0153.10.738108
MA0154.11.95784
MA0155.10.365082
MA0156.10.140505
MA0157.10.442323
MA0158.10
MA0159.10.29763
MA0160.10.26995
MA0161.10
MA0162.10.0485277
MA0163.10.120807
MA0164.10.380804
MA0080.20.126365
MA0018.20.357181
MA0099.20.292649
MA0079.21.51462
MA0102.21.16862
MA0258.10.890751
MA0259.10.0929051
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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