Coexpression cluster:C1963

Full id: C1963_acute_CD14_Neutrophils_Dendritic_CD19_Eosinophils_CD34

Phase1 CAGE Peaks

Hg19::chr5:57787278..57787351,+	p1@GAPT
Hg19::chrX:30595876..30595890,-	p1@CXorf21
Hg19::chrX:30595907..30595941,-	p2@CXorf21
Hg19::chrX:30595959..30595986,-	p3@CXorf21
Hg19::chrX:30595997..30596014,-	p5@CXorf21

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:0016491	oxidoreductase activity	0.0458024255269045

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	1.40e-85	172
angioblastic mesenchymal cell	1.40e-85	172
hematopoietic oligopotent progenitor cell	1.11e-80	165
hematopoietic multipotent progenitor cell	1.11e-80	165
hematopoietic cell	8.51e-80	182
leukocyte	2.61e-72	140
hematopoietic lineage restricted progenitor cell	2.83e-60	124
myeloid cell	2.26e-58	112
common myeloid progenitor	2.26e-58	112
nongranular leukocyte	2.15e-57	119
myeloid leukocyte	9.28e-46	76
granulocyte monocyte progenitor cell	2.94e-41	71
myeloid lineage restricted progenitor cell	5.50e-40	70
macrophage dendritic cell progenitor	1.12e-37	65
monopoietic cell	2.48e-36	63
monocyte	2.48e-36	63
monoblast	2.48e-36	63
promonocyte	2.48e-36	63
CD14-positive, CD16-negative classical monocyte	3.29e-33	42
classical monocyte	1.59e-29	45
lymphocyte	2.62e-18	53
common lymphoid progenitor	2.62e-18	53
lymphoid lineage restricted progenitor cell	9.69e-18	52
lymphocyte of B lineage	2.01e-15	24
pro-B cell	2.01e-15	24
mesenchymal cell	1.83e-13	358
connective tissue cell	2.79e-12	365
B cell	9.27e-11	14
motile cell	2.29e-08	390
intermediate monocyte	1.28e-07	9
CD14-positive, CD16-positive monocyte	1.28e-07	9
granulocyte	1.34e-07	8
dendritic cell	1.64e-07	10

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.87e-46	102
blood island	1.87e-46	102
hemolymphoid system	2.94e-41	112
bone marrow	7.95e-36	80
bone element	4.02e-31	86
immune system	2.87e-26	115
adult organism	6.05e-25	115
skeletal element	9.72e-23	101
skeletal system	9.72e-23	101
connective tissue	4.24e-11	375
lateral plate mesoderm	3.54e-09	216
neural tube	3.88e-09	57
neural rod	3.88e-09	57
future spinal cord	3.88e-09	57
neural keel	3.88e-09	57
blood	5.61e-09	15
haemolymphatic fluid	5.61e-09	15
organism substance	5.61e-09	15
anterior neural tube	8.12e-08	42
regional part of forebrain	1.03e-07	41
forebrain	1.03e-07	41
future forebrain	1.03e-07	41

Disease

Ontology term	p-value	n
hematologic cancer	1.05e-13	51
immune system cancer	1.05e-13	51
leukemia	1.27e-11	39
myeloid leukemia	3.12e-11	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
BCL11A#53335	4	22.6955640828856	7.49488101632307e-06	0.00021451298395828
BCL3#602	4	27.6376822429907	3.425174836939e-06	0.000114215145209155
EBF1#1879	4	7.1251734772552	0.000723053104677421	0.00577419660493999
EP300#2033	4	5.41915338097856	0.0020938692794389	0.0121267461695403
IRF4#3662	4	17.5316101493953	2.08739444052064e-05	0.0004610943062046
MEF2A#4205	4	14.9945847277152	3.876195075647e-05	0.000728366206379087
NFKB1#4790	4	4.39045073935507	0.00470773269252496	0.0222093637489662
PAX5#5079	4	5.33565242494226	0.00222338958618779	0.0127825930304892
POU2F2#5452	4	7.28489924619402	0.000663122328874386	0.00542714778663992
RFX5#5993	4	9.63832866175608	0.00022148012581572	0.00249850538561978
SP1#6667	4	4.55870510251272	0.0040757356578168	0.0194928679015766
SPI1#6688	4	6.56345880681818	0.000995742963645402	0.00714443524183582
YY1#7528	4	3.92893659988308	0.00719386626991762	0.0298557599588288

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.