Coexpression cluster:C2322

Full id: C2322_Mast_Neutrophils_Eosinophils_granulocyte_cerebellum_Whole_CD4

Phase1 CAGE Peaks

Hg19::chr14:91526905..91526916,-	p3@RPS6KA5
Hg19::chr14:91526922..91527001,-	p1@RPS6KA5
Hg19::chr14:91527015..91527034,-	p2@RPS6KA5
Hg19::chr17:38278209..38278250,+	p2@MSL1

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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GO ID	GO name	FDR corrected p-value
GO:0016572	histone phosphorylation	0.00488637701636642
GO:0007173	epidermal growth factor receptor signaling pathway	0.0305398563522901
GO:0016570	histone modification	0.0305398563522901
GO:0016569	covalent chromatin modification	0.0305398563522901

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
hematopoietic stem cell	2.74e-22	172
angioblastic mesenchymal cell	2.74e-22	172
hematopoietic oligopotent progenitor cell	5.49e-21	165
hematopoietic multipotent progenitor cell	5.49e-21	165
leukocyte	4.29e-20	140
hematopoietic cell	3.08e-19	182
hematopoietic lineage restricted progenitor cell	1.98e-15	124
nongranular leukocyte	5.66e-14	119
lymphoid lineage restricted progenitor cell	6.15e-14	52
lymphocyte	1.00e-13	53
common lymphoid progenitor	1.00e-13	53
T cell	3.07e-09	25
pro-T cell	3.07e-09	25
mature alpha-beta T cell	4.46e-09	18
alpha-beta T cell	4.46e-09	18
immature T cell	4.46e-09	18
mature T cell	4.46e-09	18
immature alpha-beta T cell	4.46e-09	18
myeloid cell	6.47e-09	112
common myeloid progenitor	6.47e-09	112
myeloid leukocyte	7.31e-07	76

Uber Anatomy

Ontology term	p-value	n
adult organism	6.84e-34	115
neural tube	8.72e-17	57
neural rod	8.72e-17	57
future spinal cord	8.72e-17	57
neural keel	8.72e-17	57
anterior neural tube	2.50e-13	42
regional part of forebrain	3.19e-13	41
forebrain	3.19e-13	41
future forebrain	3.19e-13	41
brain	4.23e-12	69
future brain	4.23e-12	69
central nervous system	5.56e-12	82
regional part of brain	1.04e-11	59
telencephalon	2.57e-11	34
gray matter	2.79e-11	34
brain grey matter	2.79e-11	34
regional part of telencephalon	6.26e-11	33
regional part of nervous system	1.80e-10	94
nervous system	1.80e-10	94
cerebral hemisphere	2.26e-10	32
regional part of cerebral cortex	9.88e-09	22
hematopoietic system	2.63e-08	102
blood island	2.63e-08	102
neocortex	3.53e-08	20
neurectoderm	7.03e-08	90
neural plate	1.28e-07	86
presumptive neural plate	1.28e-07	86
cerebral cortex	1.59e-07	25
pallium	1.59e-07	25
blood	4.60e-07	15
haemolymphatic fluid	4.60e-07	15
organism substance	4.60e-07	15
hemolymphoid system	5.77e-07	112

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
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106384148289813
E2F4#1874	3	9.50104523646333	0.00185075103472827	0.0109253101580367
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.0099605362529511
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101352112760752
FOS#2353	3	6.7484664816708	0.00503245277631794	0.0234604443827107
FOXA2#3170	2	12.3152318763326	0.00936191628546724	0.0353386285578254
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185773927556173
IRF1#3659	3	5.72787281517293	0.00809711479033333	0.0319996432280479
IRF3#3661	3	35.2364641586172	3.79279212646878e-05	0.000719686440581891
NFYB#4801	3	12.5698449401523	0.00081145639769735	0.00618596311818347
NRF1#4899	4	12.2102794477109	4.49717228915276e-05	0.00079284297215872
PBX3#5090	3	16.4358845150581	0.000366943139555461	0.00365714042866999
RFX5#5993	3	9.03593312039632	0.00214456119132407	0.0123832490883339
SMARCB1#6598	3	13.6895368358681	0.000630578340937934	0.00518110072765454
SP2#6668	3	19.6151478703835	0.000217100426924534	0.00248533941549615
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321726810972565
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0243817341472325
ZNF143#7702	3	10.1256574141709	0.00153486161068818	0.0097624489499795
ZNF263#10127	4	8.22184163701068	0.000218787118095832	0.00248422568241037

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.