Coexpression cluster:C1261

Full id: C1261_Dendritic_CD19_CD4_CD8_CD14_Natural_Peripheral

Phase1 CAGE Peaks

Hg19::chr21:45563531..45563542,+	p@chr21:45563531..45563542 +
Hg19::chr21:45564916..45564931,-	p@chr21:45564916..45564931 -
Hg19::chr3:107843890..107843896,+	p@chr3:107843890..107843896 +
Hg19::chr3:88198926..88198939,+	p8@C3orf38
Hg19::chr4:140005443..140005527,-	p2@ELF2
Hg19::chr4:89205350..89205385,-	p4@PPM1K
Hg19::chr4:89205847..89205873,-	p2@PPM1K

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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No GOStat results

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	4.21e-57	168
angioblastic mesenchymal cell	4.21e-57	168
hematopoietic cell	1.20e-55	177
leukocyte	6.71e-51	136
hematopoietic oligopotent progenitor cell	2.19e-50	161
hematopoietic multipotent progenitor cell	2.19e-50	161
lymphocyte	2.68e-49	53
common lymphoid progenitor	2.68e-49	53
lymphoid lineage restricted progenitor cell	1.60e-48	52
nucleate cell	1.06e-46	55
nongranular leukocyte	3.84e-41	115
hematopoietic lineage restricted progenitor cell	2.63e-39	120
lymphocyte of B lineage	1.92e-23	24
pro-B cell	1.92e-23	24
T cell	2.75e-22	25
pro-T cell	2.75e-22	25
mature alpha-beta T cell	1.13e-19	18
alpha-beta T cell	1.13e-19	18
immature T cell	1.13e-19	18
mature T cell	1.13e-19	18
immature alpha-beta T cell	1.13e-19	18
B cell	9.62e-16	14
CD8-positive, alpha-beta T cell	1.03e-12	11
myeloid cell	2.73e-12	108
common myeloid progenitor	2.73e-12	108
mesenchymal cell	7.73e-10	354
connective tissue cell	4.46e-09	361
CD4-positive, alpha-beta T cell	5.94e-08	6
myeloid leukocyte	6.13e-07	72

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	6.71e-16	98
blood island	6.71e-16	98
hemolymphoid system	1.48e-14	108
blood	2.51e-13	15
haemolymphatic fluid	2.51e-13	15
organism substance	2.51e-13	15
connective tissue	2.27e-08	371
immune system	1.89e-07	93
hemopoietic organ	3.00e-07	7
immune organ	3.00e-07	7

Disease

Ontology term	p-value	n
hematologic cancer	1.27e-12	51
immune system cancer	1.27e-12	51
leukemia	7.73e-09	39
lymphoma	5.68e-07	10

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
CHD2#1106	5	7.3885877386549	0.000149868960082067	0.00193260455883578
ELF1#1997	5	3.04149854200538	0.00971956226937075	0.0365696867155707
IRF3#3661	2	13.4234149175685	0.0088581602305654	0.0336181327926167
MEF2C#4208	2	11.8032441407497	0.0113453818123496	0.0416017249877109
NFKB1#4790	6	4.70405436359472	0.00021611506140197	0.00247813360757141
PAX5#5079	6	5.71677045529528	6.92762487228137e-05	0.00109939859297401
PBX3#5090	4	12.5225786781395	0.000135673113103555	0.00177697068716105
POLR2A#5430	7	2.14745317655807	0.00474763644761028	0.0223531874020363
TAF1#6872	6	2.86546824492454	0.00372833020747146	0.0185871916816131
TBP#6908	6	3.17723201751119	0.00207411205185266	0.0120216542862223
TCF12#6938	4	6.07683708696367	0.00216549681967623	0.01249653676374
YY1#7528	5	3.50797910703847	0.00507257067280898	0.0236158431104844

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.