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Coexpression cluster:C630: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:27, 17 September 2013


Full id: C630_cervix_uterus_salivary_extraskeletal_tongue_esophagus_penis



Phase1 CAGE Peaks

Hg19::chr14:57052405..57052416,+p4@C14orf101
Hg19::chr14:80744993..80745002,-p@chr14:80744993..80745002
-
Hg19::chr15:42386758..42386763,-p1@PLA2G4D
Hg19::chr18:61214131..61214139,+p@chr18:61214131..61214139
+
Hg19::chr20:45400010..45400026,-p@chr20:45400010..45400026
-
Hg19::chr3:151879786..151879796,-p@chr3:151879786..151879796
-
Hg19::chr3:151879803..151879810,-p@chr3:151879803..151879810
-
Hg19::chr3:15205911..15205928,-p@chr3:15205911..15205928
-
Hg19::chr3:69795939..69795972,+p@chr3:69795939..69795972
+
Hg19::chr3:69796005..69796023,+p@chr3:69796005..69796023
+
Hg19::chr4:4501551..4501558,-p@chr4:4501551..4501558
-
Hg19::chr6:56362524..56362534,-p114@DST
Hg19::chr7:57928958..57928964,-p@chr7:57928958..57928964
-
Hg19::chr7:57929012..57929026,-p@chr7:57929012..57929026
-


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:0009395phospholipid catabolic process0.0251574145055594
GO:0045104intermediate filament cytoskeleton organization and biogenesis0.0251574145055594
GO:0045103intermediate filament-based process0.0251574145055594
GO:0046466membrane lipid catabolic process0.0301808989355596
GO:0044242cellular lipid catabolic process0.0402127687845839
GO:0004623phospholipase A2 activity0.0402127687845839
GO:0005509calcium ion binding0.0436812762375561



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
uterus or analog2.58e-341
embryonic uterus2.38e-1422
reproductive structure1.59e-0959
reproductive system1.59e-0959
uterus2.44e-0721
internal female genitalia4.79e-0722
male organism6.09e-0722
male reproductive system6.09e-0722
reproductive organ6.12e-0748
uterine cervix7.17e-076
neck of organ7.17e-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)
MA0003.11.06747e-05
MA0004.10.275994
MA0006.10.152601
MA0007.11.32983
MA0009.10.695988
MA0014.10.000542531
MA0017.11.02314
MA0019.10.403106
MA0024.11.45408
MA0025.10.824398
MA0027.12.28954
MA0028.10.164086
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.363295
MA0040.10.620334
MA0041.11.44251
MA0042.10.73203
MA0043.10.69629
MA0046.11.64005
MA0048.10.267987
MA0050.10.73369
MA0051.10.359609
MA0052.10.623986
MA0055.10.45122
MA0056.10
MA0057.10.254521
MA0058.10.200063
MA0059.10.199079
MA0060.10.0773489
MA0061.10.224865
MA0063.10
MA0066.11.69914
MA0067.11.00375
MA0068.10.0444239
MA0069.10.681911
MA0070.10.671241
MA0071.10.878639
MA0072.10.666958
MA0073.10.00139087
MA0074.10.358953
MA0076.10.212295
MA0077.10.65962
MA0078.10.447828
MA0081.11.09529
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.0103438
MA0089.10
MA0090.10.223576
MA0091.11.39427
MA0092.10.691297
MA0093.10.154754
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.1571
MA0103.10.146091
MA0105.10.0899037
MA0106.10.399649
MA0107.10.107387
MA0108.20.540797
MA0109.10
MA0111.10.234271
MA0113.11.87336
MA0114.10.693432
MA0115.10.929032
MA0116.10.10959
MA0117.10.732
MA0119.10.548507
MA0122.10.756889
MA0124.10.888592
MA0125.11.89135
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.369468
MA0139.10.453946
MA0140.10.327488
MA0141.10.197753
MA0142.10.514195
MA0143.10.414436
MA0144.10.0953756
MA0145.10.0609666
MA0146.10.000361686
MA0147.10.111828
MA0148.10.296708
MA0149.10.319221
MA0062.20.0599644
MA0035.20.326883
MA0039.20.00412151
MA0138.20.44894
MA0002.20.248488
MA0137.20.168782
MA0104.20.0769208
MA0047.20.388882
MA0112.20.30305
MA0065.20.333967
MA0150.10.218956
MA0151.10
MA0152.10.886132
MA0153.10.790794
MA0154.10.42076
MA0155.10.0101184
MA0156.10.170442
MA0157.10.489002
MA0158.10
MA0159.10.361202
MA0160.10.30953
MA0161.10
MA0162.10.287126
MA0163.10.00470912
MA0164.11.08899
MA0080.20.154815
MA0018.20.400879
MA0099.20.333432
MA0079.20.00309802
MA0102.21.22472
MA0258.11.54793
MA0259.10.117259
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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