Coexpression cluster:C3100

Full id: C3100_Neutrophils_occipital_Eosinophils_CD4_temporal_pineal_parietal

Phase1 CAGE Peaks

Hg19::chr11:121322987..121322998,+	p5@SORL1
Hg19::chr11:121323000..121323046,+	p1@SORL1
Hg19::chr11:121323108..121323117,+	p8@SORL1

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
leukocyte	2.74e-16	140
nongranular leukocyte	7.85e-15	119
lymphoid lineage restricted progenitor cell	1.69e-13	52
lymphocyte	3.92e-13	53
common lymphoid progenitor	3.92e-13	53
hematopoietic stem cell	7.18e-12	172
angioblastic mesenchymal cell	7.18e-12	172
hematopoietic lineage restricted progenitor cell	1.37e-11	124
hematopoietic oligopotent progenitor cell	1.75e-10	165
hematopoietic multipotent progenitor cell	1.75e-10	165
mature alpha-beta T cell	2.96e-09	18
alpha-beta T cell	2.96e-09	18
immature T cell	2.96e-09	18
mature T cell	2.96e-09	18
immature alpha-beta T cell	2.96e-09	18
hematopoietic cell	3.66e-09	182
CD8-positive, alpha-beta T cell	3.71e-07	11
T cell	6.47e-07	25
pro-T cell	6.47e-07	25

Uber Anatomy

Ontology term	p-value	n
adult organism	1.31e-35	115
neural tube	1.87e-24	57
neural rod	1.87e-24	57
future spinal cord	1.87e-24	57
neural keel	1.87e-24	57
central nervous system	3.69e-23	82
regional part of forebrain	9.00e-21	41
forebrain	9.00e-21	41
future forebrain	9.00e-21	41
anterior neural tube	1.48e-20	42
regional part of brain	2.13e-19	59
regional part of nervous system	2.31e-19	94
nervous system	2.31e-19	94
brain	2.13e-18	69
future brain	2.13e-18	69
telencephalon	4.25e-17	34
gray matter	7.84e-17	34
brain grey matter	7.84e-17	34
regional part of telencephalon	1.95e-16	33
neural plate	7.05e-16	86
presumptive neural plate	7.05e-16	86
cerebral hemisphere	7.41e-16	32
regional part of cerebral cortex	1.12e-13	22
neurectoderm	1.12e-13	90
neocortex	1.16e-12	20
pre-chordal neural plate	1.55e-12	61
cerebral cortex	1.58e-12	25
pallium	1.58e-12	25
anterior region of body	2.40e-10	129
craniocervical region	2.40e-10	129
head	1.28e-09	123
ectoderm-derived structure	9.70e-09	169
ectoderm	1.03e-07	173
presumptive ectoderm	1.03e-07	173

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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0278297218899952
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00171104951277928
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.032362455545883
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.000848828114736692
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156161186437848
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268618787179098
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172315965004794
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00661739383655431
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00308062565134349
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00540592584922585
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189536171102555
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00420465603029148
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0327958170687863
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00241921627409347
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00387714992261021

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.