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Coexpression cluster:C2230

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Full id: C2230_pons_cerebellum_merkel_occipital_paracentral_medulla_postcentral



Phase1 CAGE Peaks

Hg19::chr12:65218487..65218501,+p7@TBC1D30
Hg19::chr21:31312141..31312150,-p9@GRIK1
Hg19::chr3:56809691..56809715,-p12@ARHGEF3
Hg19::chr9:135457981..135458003,+p1@BARHL1


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


GO IDGO nameFDR corrected p-value
GO:0051966regulation of synaptic transmission, glutamatergic0.0211920527965079
GO:0035249synaptic transmission, glutamatergic0.0211920527965079
GO:0015277kainate selective glutamate receptor activity0.0278006519143408
GO:0007399nervous system development0.0278006519143408
GO:0050804regulation of synaptic transmission0.0278006519143408
GO:0051969regulation of transmission of nerve impulse0.0278006519143408
GO:0007270nerve-nerve synaptic transmission0.0278006519143408
GO:0007215glutamate signaling pathway0.0278006519143408
GO:0031644regulation of neurological process0.0294152147210372
GO:0001764neuron migration0.0344016163843688
GO:0004970ionotropic glutamate receptor activity0.0344016163843688
GO:0005234extracellular-glutamate-gated ion channel activity0.0344016163843688
GO:0050877neurological system process0.0376508935600235
GO:0050789regulation of biological process0.0457532010981795
GO:0003008system process0.0457532010981795
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0457532010981795
GO:0048731system development0.0457532010981795



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 tube2.87e-7157
neural rod2.87e-7157
future spinal cord2.87e-7157
neural keel2.87e-7157
central nervous system1.85e-6382
regional part of nervous system4.13e-6394
nervous system4.13e-6394
regional part of brain1.06e-6159
brain8.34e-5669
future brain8.34e-5669
neural plate1.11e-5286
presumptive neural plate1.11e-5286
regional part of forebrain5.78e-5041
forebrain5.78e-5041
future forebrain5.78e-5041
neurectoderm9.04e-5090
anterior neural tube1.39e-4842
gray matter2.71e-4634
brain grey matter2.71e-4634
telencephalon3.59e-4634
cerebral hemisphere7.58e-4632
regional part of cerebral cortex1.06e-4422
regional part of telencephalon8.54e-4433
neocortex2.66e-4020
cerebral cortex8.39e-3925
pallium8.39e-3925
adult organism3.40e-38115
pre-chordal neural plate2.50e-3561
ectoderm-derived structure5.23e-32169
ectoderm6.15e-31173
presumptive ectoderm6.15e-31173
head2.00e-29123
anterior region of body6.87e-29129
craniocervical region6.87e-29129
posterior neural tube4.20e-2315
chordal neural plate4.20e-2315
segmental subdivision of hindbrain9.47e-2112
hindbrain9.47e-2112
presumptive hindbrain9.47e-2112
segmental subdivision of nervous system5.77e-1913
tube3.06e-17194
gyrus1.00e-156
regional part of metencephalon6.81e-149
metencephalon6.81e-149
future metencephalon6.81e-149
parietal lobe2.15e-135
occipital lobe5.17e-135
organ part5.46e-12219
brainstem8.96e-128
epithelium9.29e-12309
anatomical cluster1.63e-11286
cell layer1.64e-11312
anatomical conduit1.73e-11241
temporal lobe8.37e-117
nucleus of brain3.02e-099
neural nucleus3.02e-099
organism subdivision6.89e-09365
medulla oblongata7.30e-093
myelencephalon7.30e-093
future myelencephalon7.30e-093
pons7.89e-093
limbic system2.77e-085
middle temporal gyrus3.07e-083
cerebellum2.30e-076
rhombic lip2.30e-076


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
SUZ12#23512337.58683568329723.12785741999833e-050.000631491013120443
ZNF263#1012736.166381227758010.006539814347975980.0279624854944839



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.