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Coexpression cluster:C1977

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Full id: C1977_peripheral_occipital_parietal_temporal_neuroblastoma_amygdala_brain



Phase1 CAGE Peaks

Hg19::chr6:40555143..40555161,-p2@LRFN2
Hg19::chr8:56014575..56014610,+p2@XKR4
Hg19::chr8:56014644..56014710,+p1@XKR4
Hg19::chr8:56015008..56015048,+p3@XKR4
Hg19::chr8:56025147..56025152,+p@chr8:56025147..56025152
+


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 cell3.65e-075
neuronal stem cell7.26e-078
Uber Anatomy
Ontology termp-valuen
central nervous system1.95e-6481
nervous system1.77e-6089
neural tube1.82e-5956
neural rod1.82e-5956
future spinal cord1.82e-5956
neural keel1.82e-5956
neurectoderm1.24e-5886
neural plate2.44e-5582
presumptive neural plate2.44e-5582
regional part of nervous system3.83e-5553
regional part of brain3.83e-5553
brain9.25e-5268
future brain9.25e-5268
regional part of forebrain4.98e-4941
forebrain4.98e-4941
anterior neural tube4.98e-4941
future forebrain4.98e-4941
pre-chordal neural plate2.66e-4561
adult organism5.70e-44114
brain grey matter5.42e-4234
gray matter5.42e-4234
telencephalon1.31e-4134
ecto-epithelium1.80e-41104
ectoderm-derived structure2.29e-40171
ectoderm2.29e-40171
presumptive ectoderm2.29e-40171
cerebral hemisphere1.72e-3932
regional part of telencephalon3.65e-3932
regional part of cerebral cortex2.24e-3422
structure with developmental contribution from neural crest1.43e-33132
cerebral cortex3.77e-3225
pallium3.77e-3225
neocortex2.33e-3120
organ system subdivision2.69e-28223
anatomical cluster2.37e-19373
organ part7.12e-13218
tube1.27e-12192
embryo2.06e-12592
multi-tissue structure1.09e-11342
posterior neural tube1.18e-1115
chordal neural plate1.18e-1115
basal ganglion1.80e-119
nuclear complex of neuraxis1.80e-119
aggregate regional part of brain1.80e-119
collection of basal ganglia1.80e-119
cerebral subcortex1.80e-119
neural nucleus3.77e-119
nucleus of brain3.77e-119
gyrus5.43e-116
occipital lobe1.59e-095
temporal lobe1.89e-096
developing anatomical structure2.03e-09581
limbic system2.84e-095
parietal lobe3.20e-095
multi-cellular organism9.73e-09656
diencephalon1.11e-087
future diencephalon1.11e-087
organ1.79e-08503
telencephalic nucleus1.89e-087
epithelium2.45e-08306
embryonic structure3.51e-08564
anatomical conduit3.68e-08240
cell layer4.28e-08309
segmental subdivision of hindbrain5.47e-0812
hindbrain5.47e-0812
presumptive hindbrain5.47e-0812
germ layer5.73e-08560
germ layer / neural crest5.73e-08560
embryonic tissue5.73e-08560
presumptive structure5.73e-08560
germ layer / neural crest derived structure5.73e-08560
epiblast (generic)5.73e-08560
corpus striatum1.43e-074
striatum1.43e-074
ventral part of telencephalon1.43e-074
future corpus striatum1.43e-074
atypical epithelium1.78e-074
segmental subdivision of nervous system3.03e-0713


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
JUN#372537.50769751540180.004511206552906030.0213381295823801
REST#597835.790017229676810.009468788694433940.0357059078010538
ZNF263#1012746.577473309608540.0009875103237900160.00709511493576675



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.