Coexpression cluster:C4657

Full id: C4657_corpus_globus_optic_thalamus_medulla_locus_substantia

Phase1 CAGE Peaks

Hg19::chr7:139477500..139477580,-	p2@HIPK2
Hg19::chr7:139477785..139477853,-	p1@HIPK2
Hg19::chr7:139477913..139477929,-	p3@HIPK2

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

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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

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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>

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Cell Type

Ontology term	p-value	n
CD14-positive, CD16-negative classical monocyte	1.96e-11	42
classical monocyte	2.21e-09	45
myeloid leukocyte	1.34e-07	76

Uber Anatomy

Ontology term	p-value	n
adult organism	4.48e-36	115
neural tube	1.52e-27	57
neural rod	1.52e-27	57
future spinal cord	1.52e-27	57
neural keel	1.52e-27	57
regional part of brain	3.98e-25	59
brain	1.00e-22	69
future brain	1.00e-22	69
anterior neural tube	6.49e-22	42
neural plate	7.56e-22	86
presumptive neural plate	7.56e-22	86
regional part of forebrain	2.51e-21	41
forebrain	2.51e-21	41
future forebrain	2.51e-21	41
central nervous system	4.48e-21	82
neurectoderm	8.68e-19	90
regional part of nervous system	4.57e-18	94
nervous system	4.57e-18	94
pre-chordal neural plate	9.24e-18	61
anterior region of body	9.74e-18	129
craniocervical region	9.74e-18	129
head	1.29e-17	123
gray matter	2.21e-17	34
brain grey matter	2.21e-17	34
telencephalon	2.45e-17	34
regional part of telencephalon	9.41e-17	33
organ	3.80e-16	511
cerebral hemisphere	5.31e-16	32
germ layer	6.84e-15	604
embryonic tissue	6.84e-15	604
presumptive structure	6.84e-15	604
epiblast (generic)	6.84e-15	604
embryonic structure	1.03e-14	605
developing anatomical structure	1.03e-14	605
anatomical group	1.04e-14	626
anatomical conduit	2.31e-14	241
anatomical system	2.66e-14	625
embryo	1.18e-13	612
ectoderm-derived structure	7.10e-13	169
anatomical cluster	8.06e-13	286
tube	8.09e-13	194
regional part of cerebral cortex	3.98e-12	22
cerebral cortex	7.56e-12	25
pallium	7.56e-12	25
ectoderm	2.27e-11	173
presumptive ectoderm	2.27e-11	173
epithelium	2.66e-11	309
cell layer	2.96e-11	312
multi-cellular organism	3.68e-11	659
neocortex	3.97e-11	20
organism subdivision	3.10e-10	365
multi-tissue structure	1.02e-09	347
tissue	7.85e-09	787
immune system	2.38e-07	115
nucleus of brain	3.45e-07	9
neural nucleus	3.45e-07	9
basal ganglion	5.58e-07	9
nuclear complex of neuraxis	5.58e-07	9
aggregate regional part of brain	5.58e-07	9
collection of basal ganglia	5.58e-07	9
cerebral subcortex	5.58e-07	9
posterior neural tube	7.12e-07	15
chordal neural plate	7.12e-07	15
hematopoietic system	8.61e-07	102
blood island	8.61e-07	102

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

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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

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322392261994785
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464836051446145
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109173664096476
NR2C2#7182	3	32.6146109052409	2.88098172333076e-05	0.000606382205165138
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00310154483638162
REST#5978	3	9.65002871612802	0.00111263624711459	0.00771085713420044
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00376369465757404
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0331148688894232
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140886316298729

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

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This analysis result is provided for C0 - C305 clusters.