Coexpression cluster:C1215

Full id: C1215_migratory_CD19_adult_immature_Dendritic_Burkitt_vein

Phase1 CAGE Peaks

Hg19::chr16:10972516..10972521,+	p@chr16:10972516..10972521 +
Hg19::chr1:151319654..151319698,-	p2@RFX5
Hg19::chr6:150954152..150954194,+	p@chr6:150954152..150954194 +
Hg19::chr6:32977327..32977330,-	p3@HLA-DOA
Hg19::chr6:32977332..32977343,-	p2@HLA-DOA
Hg19::chr6:32977345..32977394,-	p1@HLA-DOA
Hg19::chr6:33080222..33080247,+	p1@HLA-DPB2

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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p.value	FDR	nGenes	nPathway	Name
2.20729154564608e-05	0.0139721554839397	2	78	Antigen processing and presentation (KEGG):04612
0.000120772003400194	0.0382243390761613	2	182	Tuberculosis (KEGG):05152

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:0002504	antigen processing and presentation of peptide or polysaccharide antigen via MHC class II	0.00128981675613196
GO:0042613	MHC class II protein complex	0.00128981675613196
GO:0042611	MHC protein complex	0.00609127997386628
GO:0019882	antigen processing and presentation	0.00609127997386628
GO:0032395	MHC class II receptor activity	0.0174762390536148
GO:0006955	immune response	0.0328749366611706
GO:0002376	immune system process	0.0381426036666276

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
leukocyte	1.17e-56	136
nongranular leukocyte	6.80e-53	115
hematopoietic lineage restricted progenitor cell	3.23e-46	120
hematopoietic cell	4.08e-44	177
hematopoietic stem cell	1.08e-43	168
angioblastic mesenchymal cell	1.08e-43	168
hematopoietic oligopotent progenitor cell	1.11e-38	161
hematopoietic multipotent progenitor cell	1.11e-38	161
lymphocyte	1.63e-32	53
common lymphoid progenitor	1.63e-32	53
lymphoid lineage restricted progenitor cell	2.31e-31	52
nucleate cell	8.92e-31	55
lymphocyte of B lineage	1.03e-28	24
pro-B cell	1.03e-28	24
B cell	8.93e-20	14
macrophage dendritic cell progenitor	2.17e-19	61
monopoietic cell	1.31e-17	59
monocyte	1.31e-17	59
monoblast	1.31e-17	59
promonocyte	1.31e-17	59
classical monocyte	9.04e-17	42
CD14-positive, CD16-negative classical monocyte	9.04e-17	42
granulocyte monocyte progenitor cell	1.41e-16	67
defensive cell	6.13e-16	48
phagocyte	6.13e-16	48
myeloid leukocyte	1.77e-15	72
myeloid lineage restricted progenitor cell	1.47e-14	66
dendritic cell	1.80e-14	10
conventional dendritic cell	3.63e-12	8
myeloid cell	9.26e-12	108
common myeloid progenitor	9.26e-12	108
circulating cell	1.32e-08	6
immature conventional dendritic cell	4.04e-08	5
common dendritic progenitor	4.04e-08	5
Langerhans cell	5.28e-08	5
T cell	4.65e-07	25
pro-T cell	4.65e-07	25
mesenchymal cell	5.15e-07	354

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.15e-27	98
blood island	2.15e-27	98
hemolymphoid system	1.10e-25	108
immune system	3.82e-17	93
bone marrow	3.62e-14	76
bone element	2.76e-12	82
blood	1.94e-11	15
haemolymphatic fluid	1.94e-11	15
organism substance	1.94e-11	15
skeletal element	3.29e-10	90
adult organism	4.27e-10	114
skeletal system	1.01e-08	100
hemopoietic organ	4.34e-07	7
immune organ	4.34e-07	7

Disease

Ontology term	p-value	n
lymphoma	1.18e-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
NFKB1#4790	6	4.70405436359472	0.00021611506140197	0.00247758956067622
POU2F2#5452	5	6.50437432695895	0.000276785134033055	0.00294850699849839
RFX5#5993	5	8.60565059085364	7.16524263203101e-05	0.00112751359838283
SRF#6722	3	5.91307639807192	0.0106686813016745	0.0393956230408933

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.