Coexpression cluster:C4388

Full id: C4388_Wilms_Neutrophils_Eosinophils_Mast_Reticulocytes_extraskeletal_CD14

Phase1 CAGE Peaks

Hg19::chr4:160024162..160024202,+	p@chr4:160024162..160024202 +
Hg19::chr4:160024207..160024239,+	p@chr4:160024207..160024239 +
Hg19::chr4:160024245..160024256,+	p@chr4:160024245..160024256 +

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	5.16e-19	140
CD14-positive, CD16-negative classical monocyte	2.82e-18	42
hematopoietic stem cell	2.22e-16	172
angioblastic mesenchymal cell	2.22e-16	172
hematopoietic lineage restricted progenitor cell	2.80e-15	124
classical monocyte	6.98e-15	45
hematopoietic oligopotent progenitor cell	1.90e-14	165
hematopoietic multipotent progenitor cell	1.90e-14	165
hematopoietic cell	3.81e-13	182
nongranular leukocyte	8.50e-13	119
myeloid leukocyte	8.88e-13	76
granulocyte monocyte progenitor cell	4.32e-10	71
myeloid lineage restricted progenitor cell	4.99e-10	70
myeloid cell	8.83e-10	112
common myeloid progenitor	8.83e-10	112
macrophage dendritic cell progenitor	3.05e-08	65
monopoietic cell	9.90e-08	63
monocyte	9.90e-08	63
monoblast	9.90e-08	63
promonocyte	9.90e-08	63

Uber Anatomy

Ontology term	p-value	n
adult organism	3.87e-26	115
neural tube	3.09e-18	57
neural rod	3.09e-18	57
future spinal cord	3.09e-18	57
neural keel	3.09e-18	57
central nervous system	4.10e-17	82
regional part of forebrain	4.74e-17	41
forebrain	4.74e-17	41
future forebrain	4.74e-17	41
anterior neural tube	9.34e-17	42
gray matter	1.77e-15	34
brain grey matter	1.77e-15	34
telencephalon	2.20e-15	34
regional part of nervous system	4.42e-15	94
nervous system	4.42e-15	94
cerebral hemisphere	4.47e-15	32
regional part of telencephalon	7.75e-15	33
regional part of brain	4.05e-14	59
regional part of cerebral cortex	1.56e-13	22
brain	2.20e-13	69
future brain	2.20e-13	69
cerebral cortex	4.67e-13	25
pallium	4.67e-13	25
neocortex	2.24e-12	20
neurectoderm	1.93e-11	90
neural plate	2.88e-11	86
presumptive neural plate	2.88e-11	86
hematopoietic system	2.32e-10	102
blood island	2.32e-10	102
pre-chordal neural plate	1.87e-09	61
hemolymphoid system	1.51e-08	112
bone element	1.16e-07	86
bone marrow	1.19e-07	80

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
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.011558589632654
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326856611311387
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.032365903503621
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00918046597007779
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321825039043867
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.04641501937715
FOS#2353	3	8.9979553088944	0.00137249927241713	0.0090044884422371
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00243753556894971
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00583197341835335
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.015460666698399
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108986669524801
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128513028086272
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00445565131321131
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00200105112457264
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00246462800687999
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.00137170710568334
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277743390437884
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247471919935156
SP2#6668	3	26.1535304938446	5.58768218891694e-05	0.00094185271163379
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109298041794604
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330602300387412
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140660089809998
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00243443147078588
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109800343935352

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.