Coexpression cluster:C2741

Full id: C2741_B_CD14_splenic_immature_b_Mast_xeroderma

Phase1 CAGE Peaks

Hg19::chr3:47032417..47032436,+	p@chr3:47032417..47032436 +
Hg19::chr7:20259717..20259736,-	p@chr7:20259717..20259736 -
Hg19::chr9:128394685..128394703,-	p@chr9:128394685..128394703 -
Hg19::chrX:13024034..13024045,+	p@chrX:13024034..13024045 +

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><br>

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Cell Type

Ontology term	p-value	n
leukocyte	2.02e-60	140
CD14-positive, CD16-negative classical monocyte	6.80e-60	42
classical monocyte	4.04e-55	45
nongranular leukocyte	8.69e-52	119
hematopoietic lineage restricted progenitor cell	2.79e-51	124
myeloid leukocyte	9.81e-48	76
granulocyte monocyte progenitor cell	2.97e-47	71
hematopoietic cell	5.80e-47	182
hematopoietic stem cell	1.27e-45	172
angioblastic mesenchymal cell	1.27e-45	172
myeloid lineage restricted progenitor cell	1.80e-45	70
macrophage dendritic cell progenitor	4.98e-45	65
hematopoietic oligopotent progenitor cell	5.79e-45	165
hematopoietic multipotent progenitor cell	5.79e-45	165
monopoietic cell	4.13e-44	63
monocyte	4.13e-44	63
monoblast	4.13e-44	63
promonocyte	4.13e-44	63
myeloid cell	1.20e-34	112
common myeloid progenitor	1.20e-34	112
lymphocyte of B lineage	1.19e-16	24
pro-B cell	1.19e-16	24
mesenchymal cell	6.59e-13	358
connective tissue cell	2.57e-12	365
motile cell	2.97e-10	390
lymphocyte	2.01e-09	53
common lymphoid progenitor	2.01e-09	53
circulating cell	6.04e-09	6
lymphoid lineage restricted progenitor cell	1.30e-08	52
intermediate monocyte	2.06e-08	9
CD14-positive, CD16-positive monocyte	2.06e-08	9
multi fate stem cell	7.68e-08	430
conventional dendritic cell	9.20e-08	8
stem cell	1.48e-07	444
somatic stem cell	1.67e-07	436
Langerhans cell	3.60e-07	5

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	4.39e-49	102
blood island	4.39e-49	102
bone marrow	1.33e-44	80
hemolymphoid system	2.65e-43	112
bone element	1.47e-40	86
skeletal element	3.75e-34	101
skeletal system	3.75e-34	101
immune system	6.60e-33	115
lateral plate mesoderm	7.80e-17	216
musculoskeletal system	1.92e-16	167
connective tissue	1.63e-11	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
BATF#10538	3	18.2683513442277	0.000268166010572129	0.00286780565002484
BCL11A#53335	4	28.3694551036071	1.542446414682e-06	5.89862911398658e-05
BCLAF1#9774	2	10.8263238050609	0.0120220381643258	0.043662875359717
CHD2#1106	3	7.75801712558764	0.00335152246453634	0.0173059257724568
EBF1#1879	4	8.906466846569	0.0001588790747201	0.00199917731140874
EP300#2033	4	6.7739417262232	0.000474845982144264	0.00434830684166285
HNF4A#3172	2	11.5661451814768	0.0105758568176249	0.0390763429624259
HNF4G#3174	2	14.3767112632234	0.00692416998043918	0.0293095038538924
IRF4#3662	3	16.4358845150581	0.000366943139555461	0.003659585041256
MEF2A#4205	4	18.7432309096441	8.0978922767748e-06	0.000224571367895402
MEF2C#4208	3	30.983515869468	5.56692972943475e-05	0.00094185092177618
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.0076885266166853
PAX5#5079	4	6.66956553117783	0.000505277416948326	0.00444571761993818
PBX3#5090	2	10.9572563433721	0.0117453018068803	0.0428590047660381
POU2F2#5452	4	9.10612405774252	0.00014539566517493	0.00188539581266507
SP1#6667	4	5.6983813781409	0.000948260606533398	0.00685223756214914
SPI1#6688	4	8.20432350852273	0.00022066188152768	0.00249709678674498
TCF12#6938	3	7.97584867663982	0.00309092039601307	0.0162863949971853

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.