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Coexpression cluster:C3729

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Full id: C3729_medial_hippocampus_cerebral_middle_parietal_globus_olfactory



Phase1 CAGE Peaks

Hg19::chr18:55030190..55030203,+p@chr18:55030190..55030203
+
Hg19::chr3:48016734..48016748,-p49@MAP4
Hg19::chr7:98460933..98460941,-p19@TMEM130


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:0007026negative regulation of microtubule depolymerization0.0169474033792886
GO:0031114regulation of microtubule depolymerization0.0169474033792886
GO:0007019microtubule depolymerization0.0169474033792886
GO:0031111negative regulation of microtubule polymerization or depolymerization0.0169474033792886
GO:0031110regulation of microtubule polymerization or depolymerization0.0169474033792886
GO:0031109microtubule polymerization or depolymerization0.0169474033792886
GO:0051261protein depolymerization0.0206485650106885
GO:0051129negative regulation of cellular component organization and biogenesis0.0206485650106885
GO:0051128regulation of cellular component organization and biogenesis0.0300112721168847
GO:0000226microtubule cytoskeleton organization and biogenesis0.0300112721168847
GO:0051248negative regulation of protein metabolic process0.0300112721168847
GO:0005875microtubule associated complex0.0475606955091801



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 tube3.99e-6457
neural rod3.99e-6457
future spinal cord3.99e-6457
neural keel3.99e-6457
central nervous system5.51e-5482
regional part of nervous system3.77e-5394
nervous system3.77e-5394
regional part of brain1.95e-5259
regional part of forebrain1.41e-4941
forebrain1.41e-4941
future forebrain1.41e-4941
anterior neural tube3.50e-4842
brain3.00e-4769
future brain3.00e-4769
gray matter1.26e-4634
brain grey matter1.26e-4634
telencephalon4.48e-4634
neural plate1.95e-4486
presumptive neural plate1.95e-4486
regional part of telencephalon4.28e-4433
cerebral hemisphere8.25e-4332
neurectoderm7.25e-4290
adult organism1.38e-38115
regional part of cerebral cortex1.88e-3322
pre-chordal neural plate3.18e-3261
neocortex4.12e-2920
cerebral cortex6.66e-2925
pallium6.66e-2925
ectoderm-derived structure1.03e-26169
head1.15e-26123
anterior region of body4.60e-26129
craniocervical region4.60e-26129
ectoderm9.50e-26173
presumptive ectoderm9.50e-26173
nucleus of brain5.15e-209
neural nucleus5.15e-209
posterior neural tube2.30e-1615
chordal neural plate2.30e-1615
telencephalic nucleus8.67e-167
basal ganglion8.80e-169
nuclear complex of neuraxis8.80e-169
aggregate regional part of brain8.80e-169
collection of basal ganglia8.80e-169
cerebral subcortex8.80e-169
temporal lobe1.42e-147
tube5.17e-14194
brainstem6.12e-138
segmental subdivision of nervous system6.31e-1313
organ part3.86e-12219
anatomical conduit1.91e-11241
segmental subdivision of hindbrain3.86e-1112
hindbrain3.86e-1112
presumptive hindbrain3.86e-1112
gyrus2.58e-106
corpus striatum3.89e-104
striatum3.89e-104
ventral part of telencephalon3.89e-104
future corpus striatum3.89e-104
anatomical cluster6.94e-10286
epithelium1.19e-08309
middle temporal gyrus1.54e-083
cell layer1.93e-08312
caudate-putamen3.27e-083
dorsal striatum3.27e-083
limbic system3.28e-085
parietal lobe6.71e-085
occipital lobe7.20e-085
pons8.77e-083
organism subdivision1.54e-07365
brainstem nucleus1.71e-073
spinal cord1.79e-073
organ1.93e-07511
germ layer2.69e-07604
embryonic tissue2.69e-07604
presumptive structure2.69e-07604
epiblast (generic)2.69e-07604
medulla oblongata2.96e-073
myelencephalon2.96e-073
future myelencephalon2.96e-073
embryonic structure2.98e-07605
developing anatomical structure2.98e-07605
embryo6.15e-07612
anatomical system7.49e-07625
anatomical group8.28e-07626


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.