Coexpression cluster:C427

Full id: C427_Eosinophils_CD4_Peripheral_Neutrophils_Basophils_mature_Mast

Phase1 CAGE Peaks

Hg19::chr10:105880871..105880889,+	p5@SFR1
Hg19::chr11:58346375..58346390,-	p@chr11:58346375..58346390 -
Hg19::chr14:35342116..35342120,-	p@chr14:35342116..35342120 -
Hg19::chr15:72612817..72612837,+	p@chr15:72612817..72612837 +
Hg19::chr15:73075463..73075507,+	p1@LOC100287559
Hg19::chr15:93426078..93426080,+	p2@LOC100507217
Hg19::chr19:12902289..12902307,+	p1@JUNB
Hg19::chr19:39897943..39897995,+	p@chr19:39897943..39897995 +
Hg19::chr1:45273015..45273052,-	p1@TCTEX1D4
Hg19::chr22:41347007..41347050,-	p@chr22:41347007..41347050 -
Hg19::chr2:100106078..100106095,+	p@chr2:100106078..100106095 +
Hg19::chr2:208394817..208394834,+	p3@CREB1
Hg19::chr3:196229754..196229771,+	p@chr3:196229754..196229771 +
Hg19::chr3:53164571..53164592,+	p@chr3:53164571..53164592 +
Hg19::chr5:172199488..172199515,-	p@chr5:172199488..172199515 -
Hg19::chr6:30294186..30294251,+	p1@TRIM39
Hg19::chr6:36650894..36650908,+	p@chr6:36650894..36650908 +
Hg19::chr7:104654038..104654052,-	p1@LOC100216545
Hg19::chr7:130792940..130792965,+	p@chr7:130792940..130792965 +
Hg19::chr7:140624878..140624906,+	p@chr7:140624878..140624906 +
Hg19::chr9:74980291..74980312,+	p@chr9:74980291..74980312 +
Hg19::chrX:15353629..15353684,-	p1@PIGA
Hg19::chrX:15693462..15693479,-	p@chrX:15693462..15693479 -

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:0003712	transcription cofactor activity	0.018187435853225
GO:0000506	glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex	0.018187435853225
GO:0046983	protein dimerization activity	0.018187435853225
GO:0017176	phosphatidylinositol N-acetylglucosaminyltransferase activity	0.018187435853225
GO:0008134	transcription factor binding	0.0196061772370119
GO:0006506	GPI anchor biosynthetic process	0.045457632223145
GO:0006505	GPI anchor metabolic process	0.045457632223145
GO:0043565	sequence-specific DNA binding	0.045457632223145
GO:0046489	phosphoinositide biosynthetic process	0.045457632223145
GO:0005515	protein binding	0.045457632223145
GO:0008375	acetylglucosaminyltransferase activity	0.045457632223145
GO:0046474	glycerophospholipid biosynthetic process	0.045457632223145
GO:0006497	protein amino acid lipidation	0.045457632223145
GO:0042158	lipoprotein biosynthetic process	0.045457632223145
GO:0019222	regulation of metabolic process	0.045457632223145

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	2.65e-50	140
hematopoietic lineage restricted progenitor cell	1.32e-41	124
hematopoietic stem cell	7.53e-41	172
angioblastic mesenchymal cell	7.53e-41	172
nongranular leukocyte	9.64e-39	119
hematopoietic oligopotent progenitor cell	2.12e-37	165
hematopoietic multipotent progenitor cell	2.12e-37	165
hematopoietic cell	2.12e-37	182
myeloid leukocyte	1.06e-28	76
CD14-positive, CD16-negative classical monocyte	2.91e-25	42
granulocyte monocyte progenitor cell	3.57e-25	71
myeloid lineage restricted progenitor cell	2.55e-24	70
classical monocyte	7.44e-24	45
macrophage dendritic cell progenitor	1.04e-22	65
monopoietic cell	1.28e-21	63
monocyte	1.28e-21	63
monoblast	1.28e-21	63
promonocyte	1.28e-21	63
myeloid cell	2.67e-21	112
common myeloid progenitor	2.67e-21	112
lymphoid lineage restricted progenitor cell	2.52e-15	52
lymphocyte	5.92e-15	53
common lymphoid progenitor	5.92e-15	53
mature alpha-beta T cell	1.46e-09	18
alpha-beta T cell	1.46e-09	18
immature T cell	1.46e-09	18
mature T cell	1.46e-09	18
immature alpha-beta T cell	1.46e-09	18
mesenchymal cell	6.15e-09	358
connective tissue cell	5.40e-08	365
T cell	1.06e-07	25
pro-T cell	1.06e-07	25
lymphocyte of B lineage	3.06e-07	24
pro-B cell	3.06e-07	24

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	3.72e-31	102
blood island	3.72e-31	102
hemolymphoid system	9.77e-27	112
bone marrow	7.71e-24	80
bone element	8.30e-22	86
skeletal element	5.89e-16	101
skeletal system	5.89e-16	101
immune system	1.64e-15	115
blood	1.20e-07	15
haemolymphatic fluid	1.20e-07	15
organism substance	1.20e-07	15
connective tissue	1.70e-07	375

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	8	7.02060196286044	9.06157856366518e-06	0.000242165354045708
CCNT2#905	12	3.30584430102398	5.76359523990671e-05	0.000960804666018542
CEBPB#1051	11	3.8122879949597	3.80662840696668e-05	0.000718136676653166
CHD2#1106	7	3.1481808625573	0.00478415634745222	0.0224825641095915
E2F1#1869	11	2.34701223320316	0.00292051516105322	0.0157793938388638
E2F4#1874	6	3.30471138659594	0.00753827982934299	0.0310788886426951
E2F6#1876	12	2.61764646871168	0.000577650284575452	0.00484922579139744
EGR1#1958	13	2.81940557532747	0.000124671599921935	0.00166121168974827
ELF1#1997	14	2.59188571405676	0.000138567324889281	0.0018094314633798
ETS1#2113	9	3.80690644781831	0.000271333323975571	0.00289633902521307
FOS#2353	7	2.7385081374896	0.0102284132663246	0.0380822520809125
FOSL2#2355	5	3.68047839229602	0.0098682270057464	0.0370702740901067
FOXA1#3169	6	2.8908051520136	0.01416781876839	0.049706826940066
GABPB1#2553	9	2.76561541415824	0.00281600809214273	0.0154132943312874
GTF2F1#2962	10	5.53898298989463	3.88727897856282e-06	0.000126830218444899
HEY1#23462	17	2.98616903186074	1.00637621778943e-06	4.25009809177964e-05
IRF1#3659	9	2.98845538182935	0.0016253236232831	0.010172420081025
JUND#3727	12	3.64938988271532	2.09167356596463e-05	0.000461453940759992
MAX#4149	12	3.36655070035154	4.78984534698273e-05	0.000832911518803745
MXI1#4601	11	4.76422990940662	4.44187487408454e-06	0.000139060242798116
MYC#4609	15	3.40583600322352	1.72467631994131e-06	6.50500072872338e-05
NFKB1#4790	17	4.05639470483892	8.74058419112347e-09	6.71712930343446e-07
NR3C1#2908	6	3.90600608639297	0.00332273759004134	0.0171853311130752
NR4A1#3164	1	119.939649578196	0.0083048569672105	0.0327166442909923
NRF1#4899	9	4.77793543606079	4.65808628481129e-05	0.000815020729601953
PAX5#5079	10	2.8998111005121	0.000994076180607553	0.00713394641836544
PBX3#5090	6	5.71682939654195	0.000464195418708744	0.00427288078040918
POLR2A#5430	23	2.14745317655807	2.31778206774654e-08	1.63780000929216e-06
POU2F2#5452	13	5.14693968481099	1.31866051845867e-07	7.51744464450354e-06
RDBP#7936	2	13.3598612165239	0.00978099051106676	0.0367769609729731
REST#5978	7	2.93696526143027	0.0070134332091461	0.0296297055511512
RFX5#5993	7	3.66675546914633	0.00201461547972878	0.0117119079369549
SIN3A#25942	14	3.29236461632226	8.14655446505413e-06	0.000225382252126037
SMARCB1#6598	6	4.76157802986715	0.00121261701188351	0.00816218794174413
SP1#6667	12	2.97306854511699	0.000167091345775993	0.00204702088697935
SPI1#6688	11	3.92380689538044	2.89567448032055e-05	0.000605811993289659
TAF1#6872	18	2.61629709319197	2.3449581143056e-06	8.32727237334113e-05
TAF7#6879	8	3.97671979301701	0.000503213390399793	0.00443465558011678
TBP#6908	17	2.73978702959298	3.68674799878908e-06	0.000120778003213781
TCF12#6938	8	3.69894431380397	0.000818020494678032	0.00623145459107797
USF1#7391	10	2.76586925095998	0.00144690204955922	0.00927756650011763
YY1#7528	14	2.98940828251974	2.60243933511817e-05	0.000562143043889155
ZBTB7A#51341	9	2.87683407699492	0.00213244981094982	0.0123242170220679
ZNF263#10127	9	3.21724237969983	0.000952413505296	0.00685662880537734

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.