Coexpression cluster:C1662

Full id: C1662_Eosinophils_Dendritic_Neutrophils_Whole_renal_splenic_giant

Phase1 CAGE Peaks

Hg19::chr12:129308446..129308453,-	p7@SLC15A4
Hg19::chr12:129308487..129308588,-	p1@SLC15A4
Hg19::chr3:13057835..13057855,-	p@chr3:13057835..13057855 -
Hg19::chr3:44552063..44552064,-	p4@ZNF852
Hg19::chr6:42897306..42897321,+	p5@CNPY3

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:0006857	oligopeptide transport	0.00350288472860002
GO:0015833	peptide transport	0.00401801483574708

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	3.06e-32	140
nongranular leukocyte	2.18e-28	119
CD14-positive, CD16-negative classical monocyte	9.10e-25	42
macrophage dendritic cell progenitor	1.05e-22	65
monopoietic cell	7.65e-22	63
monocyte	7.65e-22	63
monoblast	7.65e-22	63
promonocyte	7.65e-22	63
myeloid leukocyte	8.97e-22	76
hematopoietic lineage restricted progenitor cell	1.21e-21	124
hematopoietic cell	1.88e-21	182
hematopoietic stem cell	3.60e-21	172
angioblastic mesenchymal cell	3.60e-21	172
classical monocyte	5.71e-21	45
hematopoietic oligopotent progenitor cell	1.01e-18	165
hematopoietic multipotent progenitor cell	1.01e-18	165
granulocyte monocyte progenitor cell	3.23e-18	71
myeloid lineage restricted progenitor cell	3.63e-15	70
connective tissue cell	4.63e-13	365
mesenchymal cell	1.80e-12	358
stem cell	2.37e-12	444
somatic cell	2.60e-12	591
myeloid cell	4.23e-12	112
common myeloid progenitor	4.23e-12	112
somatic stem cell	3.79e-11	436
motile cell	4.92e-11	390
multi fate stem cell	6.21e-11	430
lymphocyte of B lineage	1.38e-09	24
pro-B cell	1.38e-09	24
intermediate monocyte	3.38e-07	9
CD14-positive, CD16-positive monocyte	3.38e-07	9
lymphocyte	7.91e-07	53
common lymphoid progenitor	7.91e-07	53
granulocyte	8.15e-07	8
animal cell	8.68e-07	679
eukaryotic cell	8.68e-07	679

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.14e-23	102
blood island	1.14e-23	102
hemolymphoid system	1.04e-21	112
bone marrow	7.50e-17	80
immune system	2.08e-15	115
bone element	2.94e-14	86
lateral plate mesoderm	6.00e-14	216
connective tissue	3.66e-12	375
skeletal element	9.22e-12	101
skeletal system	9.22e-12	101
musculoskeletal system	1.50e-08	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	4	5.06896126157011	0.00270999809128077	0.0148900194999617
CHD2#1106	4	8.27521826729349	0.000402837356710173	0.0038768826665549
E2F1#1869	4	3.92591137190346	0.00721498454710636	0.0298674450479702
EGR1#1958	4	3.99054327584811	0.006780098300144	0.0287591051242279
ELF1#1997	5	4.25809795880754	0.000714241693977684	0.0057261601502522
ELK4#2005	3	9.74140899508082	0.0021255865657434	0.0122865915065129
ETS1#2113	4	7.78300873776187	0.000512103594768887	0.00443957726687705
FOS#2353	3	5.39877318533664	0.0115389531727874	0.0421871011136578
GABPB1#2553	4	5.65414706894574	0.00177669650209667	0.0109048193454674
MXI1#4601	3	5.97694297725558	0.00865300488936688	0.0329436853908059
NFKB1#4790	4	4.39045073935507	0.00470773269252496	0.0221953274952426
NFYA#4800	3	11.0553484198983	0.00147089290764443	0.00941059693589048
NFYB#4801	3	10.0558759521219	0.00193816560672546	0.0113866275412499
PAX5#5079	4	5.33565242494226	0.00222338958618779	0.0127741547470495
PBX3#5090	3	13.1487076120465	0.000886046932280843	0.00660230133850449
SIN3A#25942	4	4.32710778145211	0.00497705285576288	0.0232395235482192
SP2#6668	4	20.9228243950757	1.03516506540382e-05	0.000269269250973125
SREBF1#6720	2	18.8023397761953	0.00433531272958737	0.0205769735577793
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135190896205419
TCF12#6938	4	8.50757192174914	0.000361421557849226	0.00361106917442029
THAP1#55145	2	12.5476578411405	0.00952843466738653	0.0358867720240599
USF2#7392	4	10.3937579080557	0.000164617972868753	0.00202622704401175
YY1#7528	5	4.91117074985386	0.0003499314082136	0.00352493116728589
ZBTB33#10009	2	12.6658900119925	0.00935701605965159	0.0353380125932578

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.