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Coexpression cluster:C1375: Difference between revisions

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|tf_chipseq_enrich=EGR1#1958;5:4.15681591234178:0.00161796681886444:0.010131840544153!HEY1#23462;5:3.36675920258809:0.00442382704520303:0.0209485410462008!HMGN3#9324;4:5.45236514890039:0.00272961688233377:0.0149867762366763!TAF1#6872;5:2.78587190478774:0.0107863634029041:0.0397893828565943!TAF7#6879;5:9.5275578374366:2.84599232912077e-05:0.000599985048165209!ZBTB7A#51341;5:6.12659108989658:0.000247607282141475:0.00268897337418878!ZNF263#10127;5:6.8515346975089:0.000143460795381412:0.00186749370669815
|tf_chipseq_enrich=EGR1#1958;5:4.15681591234178:0.00161796681886444:0.010131840544153!HEY1#23462;5:3.36675920258809:0.00442382704520303:0.0209485410462008!HMGN3#9324;4:5.45236514890039:0.00272961688233377:0.0149867762366763!TAF1#6872;5:2.78587190478774:0.0107863634029041:0.0397893828565943!TAF7#6879;5:9.5275578374366:2.84599232912077e-05:0.000599985048165209!ZBTB7A#51341;5:6.12659108989658:0.000247607282141475:0.00268897337418878!ZNF263#10127;5:6.8515346975089:0.000143460795381412:0.00186749370669815
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}}
}}

Revision as of 14:51, 26 November 2012


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)

{{{tfbs_overrepresentation_jaspar}}}



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.