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Coexpression cluster:C931

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Full id: C931_neuroectodermal_peripheral_maxillary_gastrointestinal_Hepatocyte_small_liver



Phase1 CAGE Peaks

Hg19::chr1:214160884..214160892,-p@chr1:214160884..214160892
-
Hg19::chr1:214161272..214161322,+p1@PROX1
Hg19::chr1:214161328..214161348,+p2@PROX1
Hg19::chr1:214161358..214161377,+p3@PROX1
Hg19::chr1:214161428..214161437,+p6@PROX1
Hg19::chr1:214170889..214170891,+p@chr1:214170889..214170891
+
Hg19::chr1:214171294..214171305,+p@chr1:214171294..214171305
+
Hg19::chr1:214175769..214175774,+p@chr1:214175769..214175774
+
Hg19::chr1:214214418..214214425,+p@chr1:214214418..214214425
+


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 tube1.87e-3456
neural rod1.87e-3456
future spinal cord1.87e-3456
neural keel1.87e-3456
adult organism8.17e-33114
regional part of nervous system2.35e-3153
regional part of brain2.35e-3153
neurectoderm2.16e-3086
nervous system2.63e-2989
central nervous system3.52e-2881
neural plate6.91e-2882
presumptive neural plate6.91e-2882
brain9.57e-2768
future brain9.57e-2768
regional part of forebrain1.21e-2641
forebrain1.21e-2641
anterior neural tube1.21e-2641
future forebrain1.21e-2641
telencephalon1.23e-2234
brain grey matter1.28e-2234
gray matter1.28e-2234
organ system subdivision2.02e-21223
ecto-epithelium5.05e-21104
regional part of telencephalon1.27e-2032
pre-chordal neural plate1.55e-2061
cerebral hemisphere2.30e-2032
structure with developmental contribution from neural crest1.99e-17132
anatomical cluster3.18e-17373
regional part of cerebral cortex1.24e-1622
ectoderm-derived structure1.37e-16171
ectoderm1.37e-16171
presumptive ectoderm1.37e-16171
neocortex3.08e-1420
cerebral cortex4.95e-1425
pallium4.95e-1425
tube7.41e-14192
anatomical conduit7.92e-13240
neural nucleus1.08e-109
nucleus of brain1.08e-109
epithelium1.34e-10306
cell layer2.78e-10309
multi-tissue structure2.43e-09342
posterior neural tube6.71e-0915
chordal neural plate6.71e-0915
telencephalic nucleus1.28e-087
basal ganglion2.10e-089
nuclear complex of neuraxis2.10e-089
aggregate regional part of brain2.10e-089
collection of basal ganglia2.10e-089
cerebral subcortex2.10e-089
multi-cellular organism1.42e-07656
brainstem1.53e-076
segmental subdivision of nervous system3.06e-0713
anatomical system5.22e-07624
embryo5.95e-07592
anatomical group6.05e-07625
organ part9.27e-07218


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
CTBP2#1488427.87422237303477.62341479845092e-060.000217417208666143
FOXA1#316978.61888202729981.48686672954246e-065.7322581899847e-05
FOXA2#3170719.15702736318416.07362166732378e-094.816423487575e-07



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.