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Coexpression cluster:C1502: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;4:4.22413438464176:0.00710980547887581:0.0296163439058835!E2F4#1874;4:8.44537354352296:0.000511119352377084:0.00443398903919846!E2F6#1876;5:4.18096310974782:0.00157359875958697:0.00997542220652524!HEY1#23462;6:4.04011104310571:0.000229896855580751:0.00253379038623871!HMGN3#9324;4:5.45236514890039:0.00272961688233377:0.0149891402057972!IRF1#3659;4:5.09144250237593:0.00353524076589381:0.0179458058884603!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380581657372589!SIN3A#25942;5:4.50740393901261:0.00109611006120864:0.00766139999214086!SREBF1#6720;4:31.3372329603255:2.9644579358811e-06:0.000101376890100028!TAF1#6872;6:3.34304628574529:0.000716247428463562:0.0057356360359842!TBP#6908;6:3.70677068709639:0.00038541647290796:0.00378064346896163
|tf_chipseq_enrich=CCNT2#905;4:4.22413438464176:0.00710980547887581:0.0296163439058835!E2F4#1874;4:8.44537354352296:0.000511119352377084:0.00443398903919846!E2F6#1876;5:4.18096310974782:0.00157359875958697:0.00997542220652524!HEY1#23462;6:4.04011104310571:0.000229896855580751:0.00253379038623871!HMGN3#9324;4:5.45236514890039:0.00272961688233377:0.0149891402057972!IRF1#3659;4:5.09144250237593:0.00353524076589381:0.0179458058884603!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380581657372589!SIN3A#25942;5:4.50740393901261:0.00109611006120864:0.00766139999214086!SREBF1#6720;4:31.3372329603255:2.9644579358811e-06:0.000101376890100028!TAF1#6872;6:3.34304628574529:0.000716247428463562:0.0057356360359842!TBP#6908;6:3.70677068709639:0.00038541647290796:0.00378064346896163
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}}
}}

Revision as of 14:56, 26 November 2012


Full id: C1502_mature_Hepatocyte_argyrophil_hepatoblastoma_liver_hepatocellular_Adipocyte



Phase1 CAGE Peaks

Hg19::chr2:216946482..216946499,-p2@PECR
Hg19::chr7:73038839..73038862,-p1@MLXIPL
Hg19::chr7:73038865..73038866,-p4@MLXIPL
Hg19::chr7:73038867..73038878,-p2@MLXIPL
Hg19::chr7:73038889..73038905,-p3@MLXIPL
Hg19::chr9:130659627..130659649,-p6@ST6GALNAC6


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:0019166trans-2-enoyl-CoA reductase (NADPH) activity0.0174844729335235



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
fat cell3.99e-0715
Uber Anatomy
Ontology termp-valuen
adult organism7.08e-39114
organ system subdivision2.80e-26223
neural tube2.63e-2156
neural rod2.63e-2156
future spinal cord2.63e-2156
neural keel2.63e-2156
regional part of nervous system2.81e-2053
regional part of brain2.81e-2053
nervous system2.54e-1789
central nervous system1.65e-1681
regional part of forebrain2.15e-1641
forebrain2.15e-1641
anterior neural tube2.15e-1641
future forebrain2.15e-1641
brain7.96e-1668
future brain7.96e-1668
neurectoderm3.82e-1586
neural plate2.51e-1482
presumptive neural plate2.51e-1482
brain grey matter8.53e-1334
gray matter8.53e-1334
telencephalon1.60e-1234
cerebral hemisphere4.74e-1232
regional part of telencephalon1.18e-1132
anatomical cluster1.24e-11373
regional part of cerebral cortex1.45e-1122
subdivision of digestive tract6.16e-11118
ecto-epithelium9.55e-11104
neocortex1.66e-1020
pre-chordal neural plate2.31e-1061
multi-tissue structure1.50e-09342
cerebral cortex2.09e-0925
pallium2.09e-0925
ectoderm-derived structure1.56e-08171
ectoderm1.56e-08171
presumptive ectoderm1.56e-08171
organ2.80e-08503
digestive system5.28e-08145
digestive tract5.28e-08145
primitive gut5.28e-08145
tube5.97e-08192
anatomical conduit1.35e-07240
foregut2.56e-0787
structure with developmental contribution from neural crest3.19e-07132
immaterial anatomical entity6.95e-07117
Disease
Ontology termp-valuen
cell type cancer3.76e-14143
carcinoma1.77e-13106


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
CCNT2#90544.224134384641760.007109805478875810.0296163439058835
E2F4#187448.445373543522960.0005111193523770840.00443398903919846
E2F6#187654.180963109747820.001573598759586970.00997542220652524
HEY1#2346264.040111043105710.0002298968555807510.00253379038623871
HMGN3#932445.452365148900390.002729616882333770.0149891402057972
IRF1#365945.091442502375930.003535240765893810.0179458058884603
POLR2A#543062.147453176558070.01019570676818780.0380581657372589
SIN3A#2594254.507403939012610.001096110061208640.00766139999214086
SREBF1#6720431.33723296032552.9644579358811e-060.000101376890100028
TAF1#687263.343046285745290.0007162474284635620.0057356360359842
TBP#690863.706770687096390.000385416472907960.00378064346896163



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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