Coexpression cluster:C2609

Full id: C2609_Dendritic_anaplastic_Neutrophils_hairy_migratory_adult_acute

Phase1 CAGE Peaks

Hg19::chr20:23029233..23029266,-	p2@THBD
Hg19::chr9:139926533..139926546,-	p1@FUT7
Hg19::chr9:139926550..139926561,-	p2@FUT7
Hg19::chr9:139926567..139926578,-	p4@FUT7

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:0032496	response to lipopolysaccharide	0.00793183603597481
GO:0046920	alpha(1,3)-fucosyltransferase activity	0.00793183603597481
GO:0010165	response to X-ray	0.00793183603597481
GO:0019317	fucose catabolic process	0.00793183603597481
GO:0042355	L-fucose catabolic process	0.00793183603597481
GO:0002237	response to molecule of bacterial origin	0.00793183603597481
GO:0042354	L-fucose metabolic process	0.00793183603597481
GO:0051591	response to cAMP	0.00793183603597481
GO:0010212	response to ionizing radiation	0.00833218849866979
GO:0006004	fucose metabolic process	0.00865240253491506
GO:0008417	fucosyltransferase activity	0.00943856771636449
GO:0010033	response to organic substance	0.0297820990700115
GO:0007565	female pregnancy	0.033923185148474
GO:0007596	blood coagulation	0.033923185148474
GO:0009314	response to radiation	0.033923185148474
GO:0050817	coagulation	0.033923185148474
GO:0007599	hemostasis	0.033923185148474
GO:0009617	response to bacterium	0.033923185148474
GO:0050878	regulation of body fluid levels	0.0377176375041188
GO:0042060	wound healing	0.0377176375041188
GO:0019320	hexose catabolic process	0.0380163926467462
GO:0046365	monosaccharide catabolic process	0.0380163926467462
GO:0046164	alcohol catabolic process	0.0380163926467462
GO:0009628	response to abiotic stimulus	0.0380163926467462
GO:0006486	protein amino acid glycosylation	0.0380163926467462
GO:0043413	biopolymer glycosylation	0.0380163926467462
GO:0009101	glycoprotein biosynthetic process	0.0380163926467462
GO:0044275	cellular carbohydrate catabolic process	0.0380163926467462
GO:0016052	carbohydrate catabolic process	0.0380904031704503
GO:0051707	response to other organism	0.0385932546624681
GO:0009100	glycoprotein metabolic process	0.0385932546624681
GO:0009790	embryonic development	0.0422235260882838
GO:0019318	hexose metabolic process	0.0461195912984867
GO:0005996	monosaccharide metabolic process	0.0461195912984867
GO:0016758	transferase activity, transferring hexosyl groups	0.0461195912984867
GO:0009607	response to biotic stimulus	0.0461195912984867
GO:0022414	reproductive process	0.047346240696365

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	5.59e-60	168
angioblastic mesenchymal cell	5.59e-60	168
hematopoietic cell	3.16e-55	177
hematopoietic oligopotent progenitor cell	5.45e-54	161
hematopoietic multipotent progenitor cell	5.45e-54	161
leukocyte	4.31e-52	136
nongranular leukocyte	2.44e-35	115
hematopoietic lineage restricted progenitor cell	5.77e-34	120
myeloid cell	8.85e-29	108
common myeloid progenitor	8.85e-29	108
lymphocyte	4.77e-23	53
common lymphoid progenitor	4.77e-23	53
lymphoid lineage restricted progenitor cell	2.59e-22	52
nucleate cell	9.28e-22	55
myeloid leukocyte	1.57e-18	72
T cell	1.13e-16	25
pro-T cell	1.13e-16	25
dendritic cell	1.80e-15	10
mature alpha-beta T cell	4.52e-15	18
alpha-beta T cell	4.52e-15	18
immature T cell	4.52e-15	18
mature T cell	4.52e-15	18
immature alpha-beta T cell	4.52e-15	18
granulocyte monocyte progenitor cell	3.17e-14	67
mesenchymal cell	4.32e-13	354
conventional dendritic cell	1.19e-12	8
macrophage dendritic cell progenitor	1.59e-12	61
connective tissue cell	2.67e-12	361
granulocyte	1.76e-11	8
myeloid lineage restricted progenitor cell	2.66e-11	66
monopoietic cell	4.77e-11	59
monocyte	4.77e-11	59
monoblast	4.77e-11	59
promonocyte	4.77e-11	59
motile cell	1.40e-09	386
immature conventional dendritic cell	7.44e-09	5
common dendritic progenitor	7.44e-09	5
CD8-positive, alpha-beta T cell	4.29e-08	11
classical monocyte	5.46e-08	42
CD14-positive, CD16-negative classical monocyte	5.46e-08	42
defensive cell	7.70e-08	48
phagocyte	7.70e-08	48
blood cell	9.16e-08	11
Langerhans cell	9.86e-08	5
CD4-positive, alpha-beta T cell	1.23e-07	6
lymphocyte of B lineage	4.92e-07	24
pro-B cell	4.92e-07	24
multi fate stem cell	8.71e-07	427

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	5.69e-26	98
blood island	5.69e-26	98
hemolymphoid system	2.59e-24	108
immune system	1.54e-15	93
bone marrow	4.43e-13	76
blood	2.54e-12	15
haemolymphatic fluid	2.54e-12	15
organism substance	2.54e-12	15
connective tissue	1.17e-11	371
bone element	2.46e-11	82
skeletal element	2.06e-09	90
skeletal system	1.67e-07	100

Disease

Ontology term	p-value	n
leukemia	5.25e-10	39
hematologic cancer	8.17e-10	51
immune system cancer	8.17e-10	51
myeloid leukemia	1.69e-08	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
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.037868582378246
HDAC2#3066	3	10.0617151774697	0.0015637275447474	0.00992549781487016
SPI1#6688	3	6.15324263139204	0.00658038711305903	0.0281037478408756
TCF12#6938	3	7.97584867663982	0.00309092039601307	0.0162814664467246

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.