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Coexpression cluster:C3575: Difference between revisions

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|tf_chipseq_enrich=ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461474109480173!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00580681848192912!HNF4G#3174;2:19.1689483509645:0.00354398661128422:0.0179709855164067!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308524034557343!REST#5978;3:9.65002871612802:0.00111263624711459:0.00766609163559841!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00308682846147405!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.006423069190692!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00242462839103775
|tf_chipseq_enrich=ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461474109480173!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00580681848192912!HNF4G#3174;2:19.1689483509645:0.00354398661128422:0.0179709855164067!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308524034557343!REST#5978;3:9.65002871612802:0.00111263624711459:0.00766609163559841!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00308682846147405!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.006423069190692!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00242462839103775
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}}
}}

Revision as of 16:12, 26 November 2012


Full id: C3575_liver_Hepatocyte_testicular_Placental_colon_hepatoblastoma_acute



Phase1 CAGE Peaks

Hg19::chr16:56691838..56691862,+p3@MT1F
Hg19::chr16:56691864..56691879,+p2@MT1F
Hg19::chr16:56691911..56691929,+p4@MT1F


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
neural tube4.53e-2156
neural rod4.53e-2156
future spinal cord4.53e-2156
neural keel4.53e-2156
central nervous system8.26e-2181
adult organism1.34e-20114
regional part of nervous system2.05e-1953
regional part of brain2.05e-1953
nervous system5.43e-1789
brain1.40e-1668
future brain1.40e-1668
regional part of forebrain8.15e-1541
forebrain8.15e-1541
anterior neural tube8.15e-1541
future forebrain8.15e-1541
brain grey matter2.86e-1334
gray matter2.86e-1334
telencephalon4.55e-1334
neurectoderm8.77e-1386
neural plate9.48e-1382
presumptive neural plate9.48e-1382
organ system subdivision2.26e-12223
regional part of telencephalon2.76e-1232
cerebral hemisphere3.06e-1232
ecto-epithelium4.66e-11104
regional part of cerebral cortex5.60e-1022
pre-chordal neural plate1.56e-0961
cerebral cortex2.27e-0925
pallium2.27e-0925
neocortex5.16e-0920
posterior neural tube1.45e-0715
chordal neural plate1.45e-0715
ectoderm-derived structure2.04e-07171
ectoderm2.04e-07171
presumptive ectoderm2.04e-07171


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
ELF1#199734.258097958807540.01295179875054610.0461474109480173
FOXA1#3169311.08141974938550.000734755275698670.00580681848192912
HNF4G#3174219.16894835096450.003543986611284220.0179709855164067
NR3C1#2908314.9730233311730.0002978331194675480.00308524034557343
REST#597839.650028716128020.001112636247114590.00766609163559841
SMC3#9126315.04493284493280.0002935825420371870.00308682846147405
STAT3#6774310.51946499715420.0008589184530415310.006423069190692
ZEB1#6935316.88843201754390.0002075486917327580.00242462839103775



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.