Coexpression cluster:C1522

Full id: C1522_CD8_Natural_CD4_Basophils_thymus_Peripheral_CD19

Phase1 CAGE Peaks

Hg19::chr4:36245956..36245972,-	p6@ARAP2
Hg19::chr4:36245985..36246005,-	p3@ARAP2
Hg19::chr4:36246020..36246034,-	p10@ARAP2
Hg19::chr4:36246039..36246051,-	p11@ARAP2
Hg19::chr4:36246229..36246251,-	p7@ARAP2
Hg19::chr5:49962495..49962577,+	p1@PARP8

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:0003950	NAD+ ADP-ribosyltransferase activity	0.0134228187919463
GO:0016763	transferase activity, transferring pentosyl groups	0.0141292829388908

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	2.54e-49	136
nongranular leukocyte	2.53e-40	115
hematopoietic stem cell	3.45e-39	168
angioblastic mesenchymal cell	3.45e-39	168
hematopoietic lineage restricted progenitor cell	5.63e-38	120
hematopoietic cell	5.47e-37	177
hematopoietic oligopotent progenitor cell	4.52e-35	161
hematopoietic multipotent progenitor cell	4.52e-35	161
lymphocyte	6.44e-26	53
common lymphoid progenitor	6.44e-26	53
lymphoid lineage restricted progenitor cell	1.19e-25	52
nucleate cell	4.97e-24	55
myeloid leukocyte	8.20e-17	72
classical monocyte	1.09e-15	42
CD14-positive, CD16-negative classical monocyte	1.09e-15	42
granulocyte monocyte progenitor cell	1.20e-14	67
mature alpha-beta T cell	1.73e-14	18
alpha-beta T cell	1.73e-14	18
immature T cell	1.73e-14	18
mature T cell	1.73e-14	18
immature alpha-beta T cell	1.73e-14	18
macrophage dendritic cell progenitor	4.14e-14	61
defensive cell	7.21e-14	48
phagocyte	7.21e-14	48
T cell	1.12e-13	25
pro-T cell	1.12e-13	25
monopoietic cell	2.96e-13	59
monocyte	2.96e-13	59
monoblast	2.96e-13	59
promonocyte	2.96e-13	59
myeloid lineage restricted progenitor cell	8.55e-13	66
myeloid cell	2.20e-12	108
common myeloid progenitor	2.20e-12	108
lymphocyte of B lineage	6.86e-11	24
pro-B cell	6.86e-11	24
CD8-positive, alpha-beta T cell	1.01e-09	11
B cell	2.96e-09	14

Uber Anatomy

Ontology term	p-value	n
adult organism	5.16e-23	114
hematopoietic system	8.40e-22	98
blood island	8.40e-22	98
hemolymphoid system	1.74e-18	108
neural tube	4.29e-16	56
neural rod	4.29e-16	56
future spinal cord	4.29e-16	56
neural keel	4.29e-16	56
regional part of nervous system	1.16e-14	53
regional part of brain	1.16e-14	53
regional part of forebrain	1.51e-14	41
forebrain	1.51e-14	41
anterior neural tube	1.51e-14	41
future forebrain	1.51e-14	41
telencephalon	8.80e-13	34
brain grey matter	1.19e-12	34
gray matter	1.19e-12	34
immune system	3.37e-12	93
cerebral hemisphere	7.91e-12	32
regional part of telencephalon	9.34e-12	32
bone marrow	9.59e-12	76
regional part of cerebral cortex	1.36e-10	22
brain	4.33e-10	68
future brain	4.33e-10	68
central nervous system	7.31e-10	81
bone element	9.03e-10	82
neocortex	9.53e-10	20
blood	4.34e-09	15
haemolymphatic fluid	4.34e-09	15
organism substance	4.34e-09	15
cerebral cortex	8.52e-09	25
pallium	8.52e-09	25
neural plate	2.69e-08	82
presumptive neural plate	2.69e-08	82
pre-chordal neural plate	4.84e-08	61
skeletal element	1.23e-07	90
nervous system	2.04e-07	89
neurectoderm	4.00e-07	86
ecto-epithelium	8.84e-07	104

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
CTCF#10664	4	3.57350424871668	0.0131663500723851	0.0466128961088078
E2F1#1869	5	4.08949101239944	0.00174981759776199	0.0107607136602876
E2F6#1876	5	4.18096310974782	0.00157359875958697	0.00997602773172899
EBF1#1879	6	8.906466846569	2.00211291586927e-06	7.32394643854538e-05
EGR1#1958	5	4.15681591234178	0.00161796681886444	0.0101354868399342
ELF1#1997	5	3.54841496567295	0.00344683777572169	0.0175328409535651
EP300#2033	5	5.64495143851933	0.000368813893181486	0.00367158080163771
GATA3#2625	5	22.6970969643383	3.87517465667206e-07	1.88768360992618e-05
PAX5#5079	5	5.55797127598152	0.000397717619661286	0.0038874338305854
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380663289301386
SPI1#6688	5	6.83693625710227	0.000144964177397403	0.00188635855011306
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.00573651573476273
YY1#7528	5	4.09264229154488	0.00174336546284953	0.0107273520046275
ZEB1#6935	5	14.0736933479532	4.14824643478507e-06	0.000131603496173304

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.