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Coexpression cluster:C3789

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Full id: C3789_gall_immature_colon_small_trachea_duodenum_temporal



Phase1 CAGE Peaks

Hg19::chr19:40434161..40434170,-p@chr19:40434161..40434170
-
Hg19::chr19:40440535..40440541,-p1@FCGBP
Hg19::chr22:44854720..44854723,+p@chr22:44854720..44854723
+


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>


Cell Type
Ontology termp-valuen
Langerhans cell1.01e-125
conventional dendritic cell7.60e-078
Uber Anatomy
Ontology termp-valuen
adult organism1.53e-56115
neural tube9.51e-1857
neural rod9.51e-1857
future spinal cord9.51e-1857
neural keel9.51e-1857
anterior neural tube8.51e-1642
regional part of forebrain2.26e-1441
forebrain2.26e-1441
future forebrain2.26e-1441
telencephalon2.61e-1434
regional part of brain6.80e-1459
regional part of telencephalon4.08e-1333
neural plate6.29e-1386
presumptive neural plate6.29e-1386
gray matter7.58e-1334
brain grey matter7.58e-1334
central nervous system1.51e-1282
brain4.83e-1269
future brain4.83e-1269
neurectoderm4.84e-1290
anterior region of body8.04e-12129
craniocervical region8.04e-12129
cerebral hemisphere8.41e-1232
regional part of nervous system7.32e-1194
nervous system7.32e-1194
pre-chordal neural plate1.74e-1061
nucleus of brain3.38e-099
neural nucleus3.38e-099
basal ganglion3.64e-099
nuclear complex of neuraxis3.64e-099
aggregate regional part of brain3.64e-099
collection of basal ganglia3.64e-099
cerebral subcortex3.64e-099
head3.68e-09123
telencephalic nucleus1.78e-087
male genital duct8.47e-083
internal male genitalia8.47e-083
regional part of cerebral cortex8.98e-0822
gastrointestinal system1.71e-0735
organ1.85e-07511
brainstem1.97e-078
intestine3.29e-0727
neocortex4.40e-0720


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


No analysis results for this cluster

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.