Coexpression cluster:C4300

Full id: C4300_Basophils_Eosinophils_Mast_CD14_CD34_CD4_CD8

Phase1 CAGE Peaks

Hg19::chr3:16306114..16306133,-	p5@DPH3
Hg19::chr3:53925835..53925860,-	p2@ENST00000487571
Hg19::chr3:53925863..53925933,-	p1@ENST00000485414 p1@ENST00000487571 p1@ENST00000488746

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:0017182	peptidyl-diphthamide metabolic process	0.00147180030613446
GO:0017183	peptidyl-diphthamide biosynthetic process from peptidyl-histidine	0.00147180030613446
GO:0051099	positive regulation of binding	0.00220770045920169
GO:0050709	negative regulation of protein secretion	0.00220770045920169
GO:0018202	peptidyl-histidine modification	0.00323796067349582
GO:0051048	negative regulation of secretion	0.00417010086738098
GO:0050708	regulation of protein secretion	0.00515130107147062
GO:0051098	regulation of binding	0.00515130107147062
GO:0009306	protein secretion	0.00868362180619334
GO:0051046	regulation of secretion	0.00868362180619334
GO:0018193	peptidyl-amino acid modification	0.0161898033674791
GO:0032940	secretion by cell	0.036427057576828
GO:0046903	secretion	0.0434747167350488

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	1.37e-36	136
hematopoietic lineage restricted progenitor cell	3.67e-30	120
nongranular leukocyte	7.55e-27	115
hematopoietic stem cell	4.75e-23	168
angioblastic mesenchymal cell	4.75e-23	168
hematopoietic cell	1.00e-22	177
myeloid leukocyte	1.04e-22	72
hematopoietic oligopotent progenitor cell	6.12e-21	161
hematopoietic multipotent progenitor cell	6.12e-21	161
classical monocyte	1.07e-20	42
CD14-positive, CD16-negative classical monocyte	1.07e-20	42
myeloid lineage restricted progenitor cell	3.48e-19	66
defensive cell	5.59e-19	48
phagocyte	5.59e-19	48
granulocyte monocyte progenitor cell	4.18e-18	67
macrophage dendritic cell progenitor	1.49e-16	61
monopoietic cell	1.58e-15	59
monocyte	1.58e-15	59
monoblast	1.58e-15	59
promonocyte	1.58e-15	59
nucleate cell	3.57e-11	55
myeloid cell	4.17e-11	108
common myeloid progenitor	4.17e-11	108
lymphocyte	3.01e-10	53
common lymphoid progenitor	3.01e-10	53
lymphoid lineage restricted progenitor cell	3.66e-10	52
stuff accumulating cell	4.53e-09	87
mesenchymal cell	5.24e-09	354
connective tissue cell	6.12e-08	361
mature alpha-beta T cell	2.39e-07	18
alpha-beta T cell	2.39e-07	18
immature T cell	2.39e-07	18
mature T cell	2.39e-07	18
immature alpha-beta T cell	2.39e-07	18
motile cell	5.89e-07	386

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	4.56e-23	98
blood island	4.56e-23	98
hemolymphoid system	2.35e-18	108
bone marrow	9.85e-18	76
bone element	3.38e-16	82
adult organism	4.88e-15	114
skeletal element	4.30e-14	90
skeletal system	1.42e-12	100
immune system	4.46e-12	93
blood	4.12e-09	15
haemolymphatic fluid	4.12e-09	15
organism substance	4.12e-09	15
neural tube	1.51e-07	56
neural rod	1.51e-07	56
future spinal cord	1.51e-07	56
neural keel	1.51e-07	56
regional part of nervous system	5.57e-07	53
regional part of brain	5.57e-07	53
connective tissue	6.68e-07	371

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
ATF3#467	3	22.4631745260087	8.81932387510763e-05	0.00129894424790913
BCLAF1#9774	2	14.4350984067479	0.00620114743554613	0.0273936907630912
BRCA1#672	2	13.4561537621492	0.00711980771608456	0.0296367316883282
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190604328621622
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326602915686108
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323405869847868
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.032161591796506
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463768268834053
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00256113893233419
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154542045597581
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00388748868957941
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128456693608206
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00445341753080161
MAFF#23764	2	37.5435709932968	0.000934477401556032	0.0067709092091793
MAFK#7975	2	18.0671554252199	0.00398367474493681	0.0191155987450703
NANOG#79923	2	19.4965189873418	0.00342725564850102	0.0174553375925972
NFE2#4778	2	51.469507101086	0.000498765352839211	0.00440698432192677
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.027028508553807
NFYA#4800	2	12.2837204665537	0.00851601140372443	0.0324872599259808
NFYB#4801	2	11.1731955023576	0.0102546713505453	0.0381473774240284
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.017336837990213
SETDB1#9869	2	26.880017452007	0.00181446890796441	0.010897143086768
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277638228868093
SIX5#147912	3	17.086715355459	0.000200406054632501	0.00240107926348099
SMARCB1#6598	2	12.1684771874383	0.00867500222192174	0.033003371596069
SP1#6667	3	5.6983813781409	0.00540396270171217	0.024727675280587
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00375835759765122
THAP1#55145	3	31.3691446028513	3.23800758564397e-05	0.000648340249687635
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330404060429154

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.