Coexpression cluster:C1053

Full id: C1053_CD19_CD4_Natural_CD8_Peripheral_granulocyte_tonsil

Phase1 CAGE Peaks

Hg19::chr17:56565257..56565283,-	p2@HSF5
Hg19::chr3:122296443..122296454,+	p3@PARP15
Hg19::chr3:122296465..122296476,+	p2@PARP15
Hg19::chr3:122296477..122296503,+	p1@PARP15
Hg19::chr4:114683412..114683431,-	p10@CAMK2D
Hg19::chr6:157098579..157098634,+	p4@ARID1B
Hg19::chr6:91006503..91006517,-	p3@BACH2
Hg19::chr7:86848933..86848940,-	p5@C7orf23

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:0050794	regulation of cellular process	0.015938311957429
GO:0048096	chromatin-mediated maintenance of transcription	0.015938311957429
GO:0005954	calcium- and calmodulin-dependent protein kinase complex	0.015938311957429
GO:0050789	regulation of biological process	0.015938311957429
GO:0006355	regulation of transcription, DNA-dependent	0.015938311957429
GO:0045815	positive regulation of gene expression, epigenetic	0.015938311957429
GO:0006351	transcription, DNA-dependent	0.015938311957429
GO:0032774	RNA biosynthetic process	0.015938311957429
GO:0016514	SWI/SNF complex	0.015938311957429
GO:0065007	biological regulation	0.015938311957429
GO:0045449	regulation of transcription	0.015938311957429
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.015938311957429
GO:0006350	transcription	0.015938311957429
GO:0010468	regulation of gene expression	0.015938311957429
GO:0031323	regulation of cellular metabolic process	0.0164057432460003
GO:0019222	regulation of metabolic process	0.0178265496741685
GO:0016070	RNA metabolic process	0.0178265496741685
GO:0043283	biopolymer metabolic process	0.0207611315204404
GO:0004683	calmodulin-dependent protein kinase activity	0.0216361309010111
GO:0003950	NAD+ ADP-ribosyltransferase activity	0.0371470414944187
GO:0016585	chromatin remodeling complex	0.0381627203013111
GO:0010467	gene expression	0.0381975373612162
GO:0043565	sequence-specific DNA binding	0.0444808009532835
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0453126974446688
GO:0006338	chromatin remodeling	0.0469739915798931
GO:0005634	nucleus	0.0469739915798931
GO:0040029	regulation of gene expression, epigenetic	0.0469739915798931

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	1.52e-53	136
hematopoietic stem cell	8.01e-50	168
angioblastic mesenchymal cell	8.01e-50	168
nongranular leukocyte	1.07e-49	115
hematopoietic lineage restricted progenitor cell	1.33e-47	120
hematopoietic cell	3.91e-46	177
hematopoietic oligopotent progenitor cell	1.24e-44	161
hematopoietic multipotent progenitor cell	1.24e-44	161
lymphocyte	7.45e-34	53
common lymphoid progenitor	7.45e-34	53
lymphoid lineage restricted progenitor cell	4.14e-33	52
nucleate cell	9.22e-32	55
lymphocyte of B lineage	7.45e-20	24
pro-B cell	7.45e-20	24
granulocyte monocyte progenitor cell	8.08e-18	67
myeloid leukocyte	6.11e-17	72
myeloid lineage restricted progenitor cell	3.17e-16	66
mature alpha-beta T cell	3.08e-15	18
alpha-beta T cell	3.08e-15	18
immature T cell	3.08e-15	18
mature T cell	3.08e-15	18
immature alpha-beta T cell	3.08e-15	18
myeloid cell	5.66e-15	108
common myeloid progenitor	5.66e-15	108
monopoietic cell	7.78e-15	59
monocyte	7.78e-15	59
monoblast	7.78e-15	59
promonocyte	7.78e-15	59
macrophage dendritic cell progenitor	1.03e-14	61
B cell	1.03e-13	14
classical monocyte	8.84e-13	42
CD14-positive, CD16-negative classical monocyte	8.84e-13	42
T cell	2.61e-12	25
pro-T cell	2.61e-12	25
defensive cell	7.67e-12	48
phagocyte	7.67e-12	48
CD8-positive, alpha-beta T cell	4.30e-10	11
mesenchymal cell	4.32e-08	354
connective tissue cell	1.74e-07	361
CD4-positive, alpha-beta T cell	7.29e-07	6

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	2.19e-24	108
hematopoietic system	1.18e-23	98
blood island	1.18e-23	98
immune system	1.39e-18	93
bone marrow	3.13e-15	76
bone element	7.62e-14	82
skeletal element	1.79e-11	90
skeletal system	5.73e-10	100
adult organism	7.49e-10	114
blood	3.56e-07	15
haemolymphatic fluid	3.56e-07	15
organism substance	3.56e-07	15

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
BCLAF1#9774	4	10.8263238050609	0.000273875656269151	0.00292079032626303
NFKB1#4790	6	4.11604756814538	0.000729985658978431	0.00581621698489841
POLR2A#5430	8	2.14745317655807	0.00221072578897191	0.0127202903792869
TAF1#6872	7	2.92516550002713	0.00126532535791574	0.00849179508131102
YY1#7528	6	3.68337806239039	0.00136063115499274	0.00895700959321065

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.