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Coexpression cluster:C588: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,

Latest revision as of 11:26, 17 September 2013


Full id: C588_CD4_neuroectodermal_thymus_CD8_neuroepithelioma_Hodgkin_Peripheral



Phase1 CAGE Peaks

Hg19::chr11:60883761..60883778,+p@chr11:60883761..60883778
+
Hg19::chr14:99635843..99635847,-p@chr14:99635843..99635847
-
Hg19::chr14:99638375..99638378,-p@chr14:99638375..99638378
-
Hg19::chr14:99639180..99639182,-p7@BCL11B
Hg19::chr14:99653997..99653998,-p@chr14:99653997..99653998
-
Hg19::chr14:99701188..99701193,-p@chr14:99701188..99701193
-
Hg19::chr14:99721739..99721742,-p@chr14:99721739..99721742
-
Hg19::chr14:99736204..99736216,-p@chr14:99736204..99736216
-
Hg19::chr14:99737850..99737852,-p3@BCL11B
Hg19::chr14:99737996..99738007,-p5@BCL11B
Hg19::chr14:99738138..99738163,-p1@BCL11B
Hg19::chr14:99738457..99738468,-p@chr14:99738457..99738468
-
Hg19::chr14:99738521..99738551,-p@chr14:99738521..99738551
-
Hg19::chr8:29973082..29973088,+p@chr8:29973082..29973088
+
Hg19::chr8:77912385..77912443,+p@chr8:77912385..77912443
+


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
cerebral hemisphere4.78e-1332
telencephalon6.16e-1234
regional part of telencephalon8.11e-1232
regional part of forebrain4.44e-1141
forebrain4.44e-1141
anterior neural tube4.44e-1141
future forebrain4.44e-1141
adult organism7.84e-11114
brain grey matter8.45e-1134
gray matter8.45e-1134
regional part of cerebral cortex1.97e-1022
neocortex2.96e-1020
blood6.93e-1015
haemolymphatic fluid6.93e-1015
organism substance6.93e-1015
cerebral cortex9.85e-0925
pallium9.85e-0925
nervous system2.09e-0889
central nervous system5.80e-0881
regional part of nervous system3.34e-0753
regional part of brain3.34e-0753
hemopoietic organ9.04e-077
immune organ9.04e-077


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)
MA0003.10.0289908
MA0004.10.711841
MA0006.10.137644
MA0007.10.241375
MA0009.10.669377
MA0014.10.142864
MA0017.10.494446
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.889224
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.12.10399
MA0042.11.27338
MA0043.10.669676
MA0046.10.659066
MA0048.10.0212749
MA0050.10.246257
MA0051.10.896276
MA0052.10.598036
MA0055.10.120131
MA0056.10
MA0057.10.420982
MA0058.10.182945
MA0059.10.182001
MA0060.10.0671843
MA0061.10.0537738
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.10.341559
MA0069.10.655419
MA0070.10.644843
MA0071.10.308534
MA0072.10.640598
MA0073.10.098235
MA0074.10.894848
MA0076.11.07748
MA0077.10.633326
MA0078.10.424186
MA0081.10.18212
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.0411204
MA0089.10
MA0090.10.593146
MA0091.10.258318
MA0092.10.647316
MA0093.10.431889
MA0095.10
MA0098.10
MA0100.10.353174
MA0101.10.141917
MA0103.10.131472
MA0105.10.074747
MA0106.10.37688
MA0107.10.0950422
MA0108.20.515791
MA0109.10
MA0111.10.215855
MA0113.10.39123
MA0114.10.0920489
MA0115.10.900969
MA0116.10.0971018
MA0117.10.705104
MA0119.10.508209
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.11.12143
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.0481205
MA0140.10.30631
MA0141.10.180729
MA0142.10.489543
MA0143.10.391385
MA0144.10.0838502
MA0145.10.278475
MA0146.10.000217915
MA0147.10.326612
MA0148.12.9641
MA0149.10.298252
MA0062.20.425026
MA0035.20.824687
MA0039.20.00733764
MA0138.20.425279
MA0002.20.0612545
MA0137.20.153033
MA0104.20.0667907
MA0047.20.366327
MA0112.20.124752
MA0065.20.0514203
MA0150.10.201098
MA0151.10
MA0152.10.838393
MA0153.10.763487
MA0154.10.0156321
MA0155.10.939602
MA0156.10.469333
MA0157.10.46471
MA0158.10
MA0159.10.0995776
MA0160.10.288813
MA0161.10
MA0162.10.0243066
MA0163.10.765815
MA0164.10.402162
MA0080.20.432036
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

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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