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

Latest revision as of 12:24, 17 September 2013


Full id: C3356_Urothelial_cervical_tongue_Neutrophils_keratoacanthoma_uterus_Sebocyte



Phase1 CAGE Peaks

Hg19::chr13:20806422..20806431,-p5@GJB6
Hg19::chr13:20806445..20806465,-p1@GJB6
Hg19::chr1:17575584..17575598,+p1@PADI3


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:0000052citrulline metabolic process0.00953614299461548
GO:0019240citrulline biosynthetic process0.00953614299461548
GO:0018101peptidyl-citrulline biosynthetic process from peptidyl-arginine0.00953614299461548
GO:0004668protein-arginine deiminase activity0.00953614299461548
GO:0018195peptidyl-arginine modification0.00953614299461548
GO:0019794nonprotein amino acid metabolic process0.0123607570157109
GO:0016813hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines0.0158907641848528
GO:0005922connexon complex0.0163691689000625
GO:0042471ear morphogenesis0.0163691689000625
GO:0000051urea cycle intermediate metabolic process0.0163691689000625
GO:0005921gap junction0.0163691689000625
GO:0048839inner ear development0.0167693862056444
GO:0043583ear development0.017107839654105
GO:0014704intercalated disc0.0177757148183469
GO:0016324apical plasma membrane0.0239960942437855
GO:0045177apical part of cell0.0267705471660034
GO:0007423sensory organ development0.0267705471660034
GO:0048598embryonic morphogenesis0.0273384166545695
GO:0018193peptidyl-amino acid modification0.0332405229851315
GO:0050954sensory perception of mechanical stimulus0.0332405229851315
GO:0007605sensory perception of sound0.0332405229851315
GO:0044271nitrogen compound biosynthetic process0.0353274091037163
GO:0005911intercellular junction0.0397528999299051
GO:0016810hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds0.0409514170360427
GO:0008285negative regulation of cell proliferation0.0475291114397334
GO:0009790embryonic development0.0477251786241198



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>disease_data<br>

Cell Type
Ontology termp-valuen
endo-epithelial cell2.23e-1642
respiratory epithelial cell2.06e-1113
endodermal cell9.10e-1158
transitional epithelial cell2.61e-084
urothelial cell2.61e-084
Uber Anatomy
Ontology termp-valuen
neural tube1.31e-2156
neural rod1.31e-2156
future spinal cord1.31e-2156
neural keel1.31e-2156
regional part of nervous system1.61e-1853
regional part of brain1.61e-1853
ecto-epithelium7.28e-18104
regional part of cerebral cortex3.40e-1722
central nervous system3.95e-1781
adult organism1.24e-16114
regional part of forebrain2.97e-1641
forebrain2.97e-1641
anterior neural tube2.97e-1641
future forebrain2.97e-1641
telencephalon4.69e-1634
brain grey matter5.24e-1634
gray matter5.24e-1634
cerebral hemisphere6.61e-1632
regional part of telencephalon8.61e-1632
ectoderm-derived structure2.67e-15171
ectoderm2.67e-15171
presumptive ectoderm2.67e-15171
organ system subdivision4.39e-15223
neocortex6.92e-1520
cerebral cortex1.36e-1425
pallium1.36e-1425
brain1.68e-1468
future brain1.68e-1468
nervous system2.48e-1489
neural plate1.13e-1382
presumptive neural plate1.13e-1382
neurectoderm1.41e-1286
pre-chordal neural plate1.15e-1061
urothelium1.47e-095
structure with developmental contribution from neural crest3.95e-09132
orifice1.79e-0836
endoderm-derived structure7.52e-08160
endoderm7.52e-08160
presumptive endoderm7.52e-08160
transitional epithelium7.81e-086
organ part1.48e-07218
Disease
Ontology termp-valuen
squamous cell carcinoma3.55e-0714


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)
MA0003.12.05336
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.12.01615
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.13.923
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.12.3269
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.74132
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.90288
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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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