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Coexpression cluster:C2998

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Full id: C2998_gastrointestinal_pineal_medial_retinoblastoma_cerebral_frontal_brain



Phase1 CAGE Peaks

Hg19::chr10:16562999..16563114,-p3@C1QL3
Hg19::chr10:16563302..16563311,-p7@C1QL3
Hg19::chr10:16563446..16563457,-p6@C1QL3


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
embryonic stem cell4.22e-095
Uber Anatomy
Ontology termp-valuen
central nervous system1.39e-5682
neural tube7.95e-5557
neural rod7.95e-5557
future spinal cord7.95e-5557
neural keel7.95e-5557
regional part of nervous system9.14e-5194
nervous system9.14e-5194
brain2.38e-4769
future brain2.38e-4769
regional part of brain5.12e-4559
neural plate3.15e-4486
presumptive neural plate3.15e-4486
neurectoderm1.51e-4190
regional part of forebrain4.24e-3941
forebrain4.24e-3941
future forebrain4.24e-3941
anterior neural tube6.19e-3842
regional part of cerebral cortex3.24e-3722
gray matter3.72e-3434
brain grey matter3.72e-3434
telencephalon3.93e-3434
cerebral hemisphere4.06e-3432
neocortex7.83e-3420
regional part of telencephalon1.98e-3233
cerebral cortex4.81e-3225
pallium4.81e-3225
adult organism2.16e-29115
pre-chordal neural plate2.64e-2861
ectoderm-derived structure1.05e-25169
head4.41e-25123
ectoderm1.06e-24173
presumptive ectoderm1.06e-24173
anterior region of body2.37e-24129
craniocervical region2.37e-24129
posterior neural tube1.38e-1715
chordal neural plate1.38e-1715
segmental subdivision of hindbrain2.36e-1312
hindbrain2.36e-1312
presumptive hindbrain2.36e-1312
gyrus3.10e-126
segmental subdivision of nervous system3.86e-1213
tube8.45e-12194
temporal lobe1.40e-117
parietal lobe3.72e-105
limbic system4.91e-105
anatomical conduit5.69e-10241
occipital lobe6.24e-105
regional part of metencephalon2.97e-099
metencephalon2.97e-099
future metencephalon2.97e-099
anatomical cluster5.41e-08286
epithelium1.17e-07309
brainstem1.42e-078
cell layer1.93e-07312
middle temporal gyrus8.60e-073
organ part9.68e-07219


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.