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Coexpression cluster:C727: Difference between revisions

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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:29, 17 September 2013


Full id: C727_colon_smooth_rectum_duodenum_bladder_esophagus_prostate



Phase1 CAGE Peaks

Hg19::chr10:71175837..71175884,-p8@TACR2
Hg19::chr10:71176135..71176147,-p6@TACR2
Hg19::chr10:71176561..71176571,-p4@TACR2
Hg19::chr10:71176580..71176586,-p7@TACR2
Hg19::chr10:71176627..71176638,-p3@TACR2
Hg19::chr10:71176667..71176679,-p2@TACR2
Hg19::chr12:95775013..95775020,-p1@ENST00000549961
Hg19::chr22:31487193..31487207,+p19@SMTN
Hg19::chr22:31487784..31487801,+p@chr22:31487784..31487801
+
Hg19::chr2:74143846..74143862,+p@chr2:74143846..74143862
+
Hg19::chr9:139442039..139442067,+p1@uc004cib.1


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:0003012muscle system process0.000656532722588068
GO:0006936muscle contraction0.000656532722588068
GO:0004995tachykinin receptor activity0.00549439764808921
GO:0007217tachykinin signaling pathway0.00659298603237552
GO:0003008system process0.0161430672631361
GO:0006939smooth muscle contraction0.0161430672631361
GO:0007588excretion0.0161430672631361
GO:0008307structural constituent of muscle0.0161430672631361
GO:0008188neuropeptide receptor activity0.0161430672631361
GO:0042923neuropeptide binding0.0161430672631361
GO:0030594neurotransmitter receptor activity0.0347768246083993
GO:0042165neurotransmitter binding0.0347768246083993
GO:0001653peptide receptor activity0.0347768246083993
GO:0008528peptide receptor activity, G-protein coupled0.0347768246083993
GO:0007517muscle development0.0377085351688235
GO:0042277peptide binding0.0416847670934325
GO:0032501multicellular organismal process0.0416847670934325



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
intestine7.67e-2617
gastrointestinal system3.57e-2225
adult organism8.64e-18114
large intestine2.15e-1711
colon5.23e-149
small intestine6.52e-144
male reproductive organ8.24e-1111
male genital duct1.20e-103
internal male genitalia1.20e-103
subdivision of digestive tract9.17e-10118
vermiform appendix5.70e-091
caecum5.70e-091
midgut5.70e-091
penis6.16e-091
intromittent organ6.16e-091
lateral plate mesenchyme6.16e-091
undifferentiated genital tubercle6.16e-091
somatopleure6.16e-091
uterus or analog7.18e-091
digestive system9.80e-09145
digestive tract9.80e-09145
primitive gut9.80e-09145
vas deferens1.22e-081
spermatic cord1.22e-081
epididymis1.42e-081
male organism3.25e-0822
male reproductive system3.25e-0822
duct of male reproductive system3.34e-084
endoderm-derived structure1.16e-07160
endoderm1.16e-07160
presumptive endoderm1.16e-07160
lower digestive tract5.57e-075
reproductive structure6.79e-0759
reproductive system6.79e-0759


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)
MA0003.10.486434
MA0004.10.349539
MA0006.10.210781
MA0007.10.332734
MA0009.10.79061
MA0014.10.21986
MA0017.11.26613
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.0494179
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.10.279754
MA0056.10
MA0057.10.397382
MA0058.10.265212
MA0059.10.2641
MA0060.10.119532
MA0061.10.100525
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.0758327
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.552437
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.11.32052
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.11.10483
MA0089.10
MA0090.12.20774
MA0091.10.927876
MA0092.11.53836
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.203171
MA0105.10.15707
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.465415
MA0115.11.02805
MA0116.10.481808
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.11.3572
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.637178
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.11.24556
MA0144.10.142196
MA0145.10.277793
MA0146.10.0381286
MA0147.10.162359
MA0148.10.972544
MA0149.10.396509
MA0062.20.0969238
MA0035.20.404774
MA0039.20.396868
MA0138.22.2748
MA0002.20.111226
MA0137.20.229531
MA0104.20.118985
MA0047.21.18756
MA0112.20.106997
MA0065.20.839576
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.634487
MA0155.10.462858
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.489747
MA0160.10.386031
MA0161.10
MA0162.10.00470038
MA0163.10.826158
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.20.395456
MA0102.21.32663
MA0258.10.420151
MA0259.10.168926
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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