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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4133_occipital_parietal_temporal_optic_CD14_rectum_ovary
|full_id=C4133_occipital_parietal_temporal_optic_CD14_rectum_ovary
|id=C4133
|id=C4133

Revision as of 17:10, 12 September 2012


Full id: C4133_occipital_parietal_temporal_optic_CD14_rectum_ovary



Phase1 CAGE Peaks

Hg19::chr2:145277792..145277808,-p15@ZEB2
Hg19::chr2:145277820..145277831,-p18@ZEB2
Hg19::chr2:145277833..145277845,-p16@ZEB2


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><br>

Uber Anatomy
Ontology termp-valuen
adult organism1.51e-32115
neural tube3.19e-2057
neural rod3.19e-2057
future spinal cord3.19e-2057
neural keel3.19e-2057
hematopoietic system3.25e-20102
blood island3.25e-20102
bone marrow1.79e-1980
central nervous system8.75e-1982
regional part of brain1.72e-1859
bone element1.89e-1886
skeletal element6.08e-18101
skeletal system6.08e-18101
brain4.33e-1769
future brain4.33e-1769
hemolymphoid system5.66e-17112
anterior neural tube7.07e-1742
regional part of nervous system1.29e-1694
nervous system1.29e-1694
regional part of forebrain2.17e-1641
forebrain2.17e-1641
future forebrain2.17e-1641
telencephalon1.91e-1534
gray matter3.81e-1534
brain grey matter3.81e-1534
regional part of telencephalon8.23e-1533
cerebral hemisphere3.84e-1432
neurectoderm7.26e-1390
regional part of cerebral cortex4.32e-1222
neural plate1.41e-1186
presumptive neural plate1.41e-1186
neocortex1.49e-1120
cerebral cortex2.12e-1125
pallium2.12e-1125
musculoskeletal system6.57e-11167
immune system2.65e-10115
pre-chordal neural plate4.02e-0961
tissue1.54e-08787
head5.95e-08123
ectoderm7.22e-08173
presumptive ectoderm7.22e-08173
anterior region of body7.38e-08129
craniocervical region7.38e-08129
organ4.43e-07511
ectoderm-derived structure5.32e-07169


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
BCLAF1#9774321.65264761012189.8473954032885e-050.00139356656981578
CCNT2#90536.336201576962630.003930750035764890.0190436332970844
CTCF#1066435.360256373075030.0064925092527670.0280044262937155
CTCFL#140690319.74647435897440.0001298372005551160.00172038408890837
E2F6#187635.017155731697390.00791769806886330.0323039483011959
ELF1#199734.258097958807540.01295179875054610.0463355225467846
EP300#203336.77394172622320.003216880500103790.0167740667307574
GATA2#2624312.7449317335540.0004829527704283790.00437535603667328
GTF2B#2959331.94382993432423.06634405746243e-050.000628672766033214
IRF1#365937.63716375356390.002244692747297240.0128358227023093
JUND#372736.994663941871030.002921845042734990.0157061389890473
RAD21#5885310.35503389545630.0009004912073565420.00665438344336729
REST#597839.650028716128020.001112636247114590.0076904445408604
SIRT6#515483153.6384039900252.75057764221434e-071.40062203010836e-05
TRIM28#10155318.59052504526250.0001555969297255280.00197405098926195
USF1#739136.361499277207960.00388404057290560.0190712418144658
YY1#752834.911170749853860.008441455341808260.0330033000577664
ZBTB7A#5134137.35190930787590.002516255860282270.0140524702311117



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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