Coexpression cluster:C3885

Full id: C3885_B_chronic_NK_cord_plasma_CD4_acute

Phase1 CAGE Peaks

Hg19::chr1:158978768..158978800,+	p8@IFI16
Hg19::chr1:158978805..158978820,+	p23@IFI16
Hg19::chr1:158978830..158978851,+	p22@IFI16

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	6.98e-49	172
angioblastic mesenchymal cell	6.98e-49	172
hematopoietic cell	1.73e-47	182
hematopoietic oligopotent progenitor cell	7.07e-46	165
hematopoietic multipotent progenitor cell	7.07e-46	165
leukocyte	1.62e-40	140
nongranular leukocyte	2.69e-38	119
hematopoietic lineage restricted progenitor cell	2.00e-37	124
lymphocyte	9.29e-36	53
common lymphoid progenitor	9.29e-36	53
lymphoid lineage restricted progenitor cell	5.67e-35	52
T cell	3.38e-18	25
pro-T cell	3.38e-18	25
lymphocyte of B lineage	1.16e-15	24
pro-B cell	1.16e-15	24
myeloid cell	4.85e-15	112
common myeloid progenitor	4.85e-15	112
mesenchymal cell	1.96e-14	358
motile cell	1.13e-13	390
connective tissue cell	2.98e-13	365
mature alpha-beta T cell	4.17e-13	18
alpha-beta T cell	4.17e-13	18
immature T cell	4.17e-13	18
mature T cell	4.17e-13	18
immature alpha-beta T cell	4.17e-13	18
CD14-positive, CD16-negative classical monocyte	7.45e-11	42
classical monocyte	4.64e-10	45
myeloid leukocyte	1.43e-09	76
myeloid lineage restricted progenitor cell	2.20e-09	70
CD8-positive, alpha-beta T cell	2.66e-09	11
B cell	4.40e-09	14
granulocyte monocyte progenitor cell	1.52e-08	71
multi fate stem cell	4.62e-08	430
monopoietic cell	1.46e-07	63
monocyte	1.46e-07	63
monoblast	1.46e-07	63
promonocyte	1.46e-07	63
stem cell	1.60e-07	444
somatic stem cell	2.17e-07	436
macrophage dendritic cell progenitor	5.45e-07	65

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.46e-17	102
blood island	2.46e-17	102
hemolymphoid system	2.70e-15	112
connective tissue	2.72e-13	375
blood	8.19e-10	15
haemolymphatic fluid	8.19e-10	15
organism substance	8.19e-10	15
bone marrow	3.85e-08	80
immune system	1.76e-07	115
bone element	2.13e-07	86

Disease

Ontology term	p-value	n
hematologic cancer	4.02e-16	51
immune system cancer	4.02e-16	51
leukemia	8.08e-11	39
lymphoma	5.20e-08	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
BCL11A#53335	3	28.3694551036071	4.37778126761649e-05	0.000777834463777813
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00915657924162138
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167506497756564
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00762687829911008
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269708169667124
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172993474082319
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00882486685971086
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246628413128875
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00629536058593905
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329564186177381

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.