Coexpression cluster:C3615

Full id: C3615_CD4_CD8_Natural_Mast_CD19_granulocyte_Basophils

Phase1 CAGE Peaks

Hg19::chr17:2207011..2207061,-	p3@SMG6
Hg19::chr4:68411097..68411110,-	p4@CENPC1
Hg19::chr4:68411152..68411174,-	p2@CENPC1

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:0044427	chromosomal part	0.00640195440246109
GO:0005694	chromosome	0.00640195440246109
GO:0005697	telomerase holoenzyme complex	0.00640195440246109
GO:0035303	regulation of dephosphorylation	0.00640195440246109
GO:0042162	telomeric DNA binding	0.0122082852453962
GO:0000184	mRNA catabolic process, nonsense-mediated decay	0.0122082852453962
GO:0006406	mRNA export from nucleus	0.0122082852453962
GO:0032200	telomere organization and biogenesis	0.0122082852453962
GO:0006402	mRNA catabolic process	0.0122082852453962
GO:0000723	telomere maintenance	0.0122082852453962
GO:0006405	RNA export from nucleus	0.0122082852453962
GO:0000781	chromosome, telomeric region	0.0122082852453962
GO:0000776	kinetochore	0.0122082852453962
GO:0051168	nuclear export	0.0156966496204888
GO:0006401	RNA catabolic process	0.0156966496204888
GO:0051174	regulation of phosphorus metabolic process	0.0204600198138956
GO:0019220	regulation of phosphate metabolic process	0.0204600198138956
GO:0000775	chromosome, pericentric region	0.0204600198138956
GO:0051028	mRNA transport	0.0204600198138956
GO:0050658	RNA transport	0.0204600198138956
GO:0051236	establishment of RNA localization	0.0204600198138956
GO:0050657	nucleic acid transport	0.0204600198138956
GO:0006403	RNA localization	0.0204600198138956
GO:0015931	nucleobase, nucleoside, nucleotide and nucleic acid transport	0.0221611014011255
GO:0043232	intracellular non-membrane-bound organelle	0.024713451545318
GO:0043228	non-membrane-bound organelle	0.024713451545318
GO:0030145	manganese ion binding	0.0265729373489249
GO:0004519	endonuclease activity	0.0265729373489249
GO:0006913	nucleocytoplasmic transport	0.0265729373489249
GO:0051169	nuclear transport	0.0265729373489249
GO:0003677	DNA binding	0.0298832650009259
GO:0032991	macromolecular complex	0.0355109874751774
GO:0004518	nuclease activity	0.0367296420604185
GO:0044446	intracellular organelle part	0.0367296420604185
GO:0044422	organelle part	0.0367296420604185
GO:0016311	dephosphorylation	0.0396731410028892
GO:0016071	mRNA metabolic process	0.0471050325502772

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
hematopoietic stem cell	3.81e-53	168
angioblastic mesenchymal cell	3.81e-53	168
hematopoietic cell	3.72e-50	177
hematopoietic oligopotent progenitor cell	1.93e-48	161
hematopoietic multipotent progenitor cell	1.93e-48	161
leukocyte	4.20e-40	136
hematopoietic lineage restricted progenitor cell	2.66e-32	120
nongranular leukocyte	3.51e-32	115
myeloid cell	8.08e-25	108
common myeloid progenitor	8.08e-25	108
lymphocyte	3.60e-22	53
common lymphoid progenitor	3.60e-22	53
lymphoid lineage restricted progenitor cell	1.00e-21	52
nucleate cell	8.61e-21	55
myeloid leukocyte	1.51e-14	72
granulocyte monocyte progenitor cell	3.97e-13	67
classical monocyte	2.04e-12	42
CD14-positive, CD16-negative classical monocyte	2.04e-12	42
T cell	4.15e-12	25
pro-T cell	4.15e-12	25
myeloid lineage restricted progenitor cell	2.61e-11	66
mature alpha-beta T cell	2.69e-11	18
alpha-beta T cell	2.69e-11	18
immature T cell	2.69e-11	18
mature T cell	2.69e-11	18
immature alpha-beta T cell	2.69e-11	18
macrophage dendritic cell progenitor	2.17e-10	61
monopoietic cell	7.56e-10	59
monocyte	7.56e-10	59
monoblast	7.56e-10	59
promonocyte	7.56e-10	59
defensive cell	2.13e-09	48
phagocyte	2.13e-09	48
mesenchymal cell	4.17e-09	354
lymphocyte of B lineage	5.09e-09	24
pro-B cell	5.09e-09	24
connective tissue cell	4.70e-08	361
motile cell	1.51e-07	386
CD8-positive, alpha-beta T cell	3.31e-07	11

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.04e-15	98
blood island	1.04e-15	98
hemolymphoid system	3.67e-15	108
immune system	2.17e-11	93
bone marrow	3.21e-10	76
bone element	5.38e-10	82
connective tissue	1.97e-08	371
skeletal element	7.99e-08	90

Disease

Ontology term	p-value	n
hematologic cancer	1.94e-16	51
immune system cancer	1.94e-16	51
leukemia	1.68e-14	39
myeloid leukemia	1.88e-12	31

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
BRCA1#672	2	13.4561537621492	0.00711980771608456	0.0296213838210634
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324849955400461
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321657254011986
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320196196278328
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461663109115455
FOXA2#3170	2	16.4203091684435	0.00481068235210548	0.0225858779128588
GTF2B#2959	2	21.2958866228828	0.00287818058991141	0.0155788703099123
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127923969134005
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294158904403156
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269340234235085
NFYA#4800	2	12.2837204665537	0.00851601140372443	0.0324682844154921
NFYB#4801	2	11.1731955023576	0.0102546713505453	0.0381202214336927
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00470817527201945
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172772700002598
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276289906229363
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328900262802877
ZBTB33#10009	2	21.1098166866541	0.00292859706060324	0.0156330052855784

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.