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

Latest revision as of 11:43, 17 September 2013


Full id: C1375_cerebellum_Pericytes_extraskeletal_neuroblastoma_teratocarcinoma_neuroectodermal_H9



Phase1 CAGE Peaks

Hg19::chr13:100633838..100633854,-p@chr13:100633838..100633854
-
Hg19::chr13:100634004..100634025,+p2@ZIC2
Hg19::chr13:100634088..100634099,+p5@ZIC2
Hg19::chr13:100634111..100634118,+p8@ZIC2
Hg19::chr13:100634130..100634143,+p3@ZIC2
Hg19::chr3:147124697..147124729,+p@chr3:147124697..147124729
+


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>disease_data<br>

Cell Type
Ontology termp-valuen
neural cell1.07e-1125
neurectodermal cell1.13e-0859
neuronal stem cell1.82e-078
embryonic stem cell9.88e-075
Uber Anatomy
Ontology termp-valuen
central nervous system1.24e-2981
nervous system1.03e-2889
brain3.53e-2168
future brain3.53e-2168
neurectoderm9.61e-2086
neural tube1.46e-1956
neural rod1.46e-1956
future spinal cord1.46e-1956
neural keel1.46e-1956
regional part of nervous system4.19e-1853
regional part of brain4.19e-1853
neural plate8.04e-1782
presumptive neural plate8.04e-1782
ectoderm-derived structure1.15e-16171
ectoderm1.15e-16171
presumptive ectoderm1.15e-16171
posterior neural tube1.99e-1215
chordal neural plate1.99e-1215
ecto-epithelium8.76e-12104
segmental subdivision of hindbrain4.37e-1112
hindbrain4.37e-1112
presumptive hindbrain4.37e-1112
organ system subdivision5.19e-11223
pre-chordal neural plate8.92e-1161
regional part of forebrain3.95e-1041
forebrain3.95e-1041
anterior neural tube3.95e-1041
future forebrain3.95e-1041
segmental subdivision of nervous system6.33e-1013
telencephalon9.02e-0934
regional part of metencephalon9.37e-099
metencephalon9.37e-099
future metencephalon9.37e-099
structure with developmental contribution from neural crest1.11e-08132
brain grey matter2.50e-0834
gray matter2.50e-0834
cerebral hemisphere6.91e-0832
cerebral cortex6.96e-0825
pallium6.96e-0825
regional part of telencephalon8.76e-0832
cerebellum1.12e-076
rhombic lip1.12e-076
Disease
Ontology termp-valuen
cancer1.69e-32235
disease of cellular proliferation5.78e-31239
cell type cancer1.31e-30143
carcinoma1.18e-20106
adenocarcinoma1.74e-0925
organ system cancer2.00e-09137
sarcoma7.41e-0820


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)
MA0003.12.14318
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.13.70108
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.12.08744
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.213007
MA0056.10
MA0057.10.450439
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.959858
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.12.02016
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.11.22966
MA0091.10.561458
MA0092.11.29635
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.865577
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.718193
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.35955
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.12.97671
MA0163.14.41596
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.218.7822
MA0102.21.58513
MA0258.10.289793
MA0259.12.42942
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
EGR1#195854.156815912341780.001617966818864440.010131840544153
HEY1#2346253.366759202588090.004423827045203030.0209485410462008
HMGN3#932445.452365148900390.002729616882333770.0149867762366763
TAF1#687252.785871904787740.01078636340290410.0397893828565943
TAF7#687959.52755783743662.84599232912077e-050.000599985048165209
ZBTB7A#5134156.126591089896580.0002476072821414750.00268897337418878
ZNF263#1012756.85153469750890.0001434607953814120.00186749370669815



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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