Coexpression cluster:C675

Full id: C675_Eosinophils_CD14_Natural_CD8_Neutrophils_Basophils_CD4

Phase1 CAGE Peaks

Hg19::chr10:27444086..27444105,-	p4@YME1L1
Hg19::chr12:49412702..49412735,+	p@chr12:49412702..49412735 +
Hg19::chr12:50064927..50064942,+	p@chr12:50064927..50064942 +
Hg19::chr17:75954523..75954527,-	p@chr17:75954523..75954527 -
Hg19::chr19:41304544..41304552,-	p@chr19:41304544..41304552 -
Hg19::chr19:54372647..54372650,-	p7@ENST00000455835
Hg19::chr1:174968433..174968454,-	p4@BC038430
Hg19::chr21:45559862..45559873,-	p1@AK127364
Hg19::chr2:135810397..135810416,+	p@chr2:135810397..135810416 +
Hg19::chr6:138029264..138029275,-	p@chr6:138029264..138029275 -
Hg19::chr7:130598148..130598162,-	p2@LOC646329
Hg19::chr9:134609727..134609746,-	p@chr9:134609727..134609746 -

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:0005618	cell wall	0.00541614540821025
GO:0030312	external encapsulating structure	0.00812373980212789
GO:0005739	mitochondrion	0.0132731077032574

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	2.34e-87	136
nongranular leukocyte	3.66e-73	115
hematopoietic lineage restricted progenitor cell	6.24e-73	120
hematopoietic stem cell	4.02e-69	168
angioblastic mesenchymal cell	4.02e-69	168
hematopoietic cell	2.15e-67	177
classical monocyte	5.42e-65	42
CD14-positive, CD16-negative classical monocyte	5.42e-65	42
hematopoietic oligopotent progenitor cell	2.53e-60	161
hematopoietic multipotent progenitor cell	2.53e-60	161
defensive cell	5.25e-55	48
phagocyte	5.25e-55	48
myeloid leukocyte	3.98e-54	72
granulocyte monocyte progenitor cell	9.09e-49	67
macrophage dendritic cell progenitor	8.27e-48	61
myeloid lineage restricted progenitor cell	2.36e-45	66
monopoietic cell	2.64e-45	59
monocyte	2.64e-45	59
monoblast	2.64e-45	59
promonocyte	2.64e-45	59
myeloid cell	9.15e-35	108
common myeloid progenitor	9.15e-35	108
stuff accumulating cell	5.37e-24	87
lymphoid lineage restricted progenitor cell	4.30e-23	52
lymphocyte	1.81e-22	53
common lymphoid progenitor	1.81e-22	53
mesenchymal cell	1.19e-21	354
nucleate cell	2.72e-21	55
connective tissue cell	1.02e-20	361
motile cell	1.90e-17	386
stem cell	4.44e-14	441
intermediate monocyte	5.89e-14	9
CD14-positive, CD16-positive monocyte	5.89e-14	9
multi fate stem cell	1.66e-13	427
somatic stem cell	5.74e-13	433
T cell	1.30e-11	25
pro-T cell	1.30e-11	25
mature alpha-beta T cell	1.53e-11	18
alpha-beta T cell	1.53e-11	18
immature T cell	1.53e-11	18
mature T cell	1.53e-11	18
immature alpha-beta T cell	1.53e-11	18
CD4-positive, alpha-beta T cell	4.57e-11	6
lymphocyte of B lineage	6.18e-09	24
pro-B cell	6.18e-09	24
granulocyte	8.00e-08	8
blood cell	4.99e-07	11
natural killer cell	6.51e-07	3
pro-NK cell	6.51e-07	3

Uber Anatomy

Ontology term	p-value	n
bone marrow	6.42e-45	76
hematopoietic system	1.62e-44	98
blood island	1.62e-44	98
bone element	1.90e-40	82
immune system	2.83e-40	93
hemolymphoid system	4.19e-40	108
skeletal element	2.01e-35	90
skeletal system	2.75e-30	100
connective tissue	1.90e-19	371
lateral plate mesoderm	3.43e-13	203
musculoskeletal system	3.52e-12	167

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
CCNT2#905	6	3.16810078848132	0.00601562194267421	0.0269653435800228
E2F1#1869	7	2.86264370867961	0.00436076322914768	0.0206724048335961
E2F4#1874	4	4.22268677176148	0.0114651023744674	0.0419391204121398
E2F6#1876	7	2.92667417682348	0.00382308432247255	0.0188713065296678
EBF1#1879	6	4.4532334232845	0.00101188147698625	0.00717934032438631
EGR1#1958	7	2.90977113863925	0.00395734076047912	0.0189962178463795
ELF1#1997	8	2.83873197253836	0.00180427034609404	0.0109149786072588
ETS1#2113	6	4.86438046110117	0.000628137752643445	0.00516958855384782
GTF2B#2959	3	7.98595748358106	0.00545549118698288	0.02471655579027
GTF2F1#2962	4	4.24655362558588	0.0112427702155768	0.0412761865414498
HEY1#23462	7	2.35673144181166	0.0134698206126472	0.0475776039963561
HMGN3#9324	5	3.40772821806275	0.0102804055907503	0.0381941332393856
IRF1#3659	7	4.45501218957894	0.000285027758631937	0.00303105733466662
MAX#4149	6	3.22627775450356	0.0054834811269129	0.0248325941121176
MYC#4609	7	3.04633109177215	0.00300767491317981	0.0159816107991649
NFKB1#4790	8	3.65870894946256	0.000297373752167086	0.0031041896354401
PAX5#5079	6	3.33478276558891	0.00462982151105892	0.021860569139359
POLR2A#5430	11	1.96849874517823	0.0015351588645567	0.00975958465153622
POU2F2#5452	7	5.31190570034981	9.21465586752959e-05	0.00134202962508565
SIN3A#25942	7	3.15518275730883	0.00243377588228146	0.0137069197244173
SP1#6667	7	3.32405580391552	0.00177269703194813	0.0108879502069884
SPI1#6688	5	3.41846812855114	0.0101446127953198	0.0378958872498179
SRF#6722	4	4.5990594207226	0.00850662993893072	0.0324668880350821
WRNIP1#56897	2	18.3033273915627	0.00514758052362029	0.0239287916636124

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.