Coexpression cluster:C3488

Full id: C3488_thymus_CD4_giant_Peripheral_CD8_CD19_Dendritic

Phase1 CAGE Peaks

Hg19::chr15:43478059..43478094,-	p@chr15:43478059..43478094 -
Hg19::chr3:195163834..195163851,-	p6@ACAP2
Hg19::chr3:195163852..195163868,-	p5@ACAP2

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><br>

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Cell Type

Ontology term	p-value	n
lymphoid lineage restricted progenitor cell	1.87e-17	52
lymphocyte	2.00e-17	53
common lymphoid progenitor	2.00e-17	53
hematopoietic stem cell	1.46e-15	172
angioblastic mesenchymal cell	1.46e-15	172
leukocyte	3.44e-14	140
hematopoietic cell	1.70e-13	182
hematopoietic oligopotent progenitor cell	6.64e-13	165
hematopoietic multipotent progenitor cell	6.64e-13	165
mature alpha-beta T cell	4.67e-12	18
alpha-beta T cell	4.67e-12	18
immature T cell	4.67e-12	18
mature T cell	4.67e-12	18
immature alpha-beta T cell	4.67e-12	18
T cell	1.08e-11	25
pro-T cell	1.08e-11	25
nongranular leukocyte	1.50e-10	119
hematopoietic lineage restricted progenitor cell	8.08e-10	124
CD8-positive, alpha-beta T cell	3.06e-08	11
B cell	6.59e-08	14

Uber Anatomy

Ontology term	p-value	n
adult organism	3.19e-20	115
regional part of nervous system	1.56e-15	94
nervous system	1.56e-15	94
central nervous system	3.09e-14	82
neural tube	7.67e-14	57
neural rod	7.67e-14	57
future spinal cord	7.67e-14	57
neural keel	7.67e-14	57
brain	1.00e-12	69
future brain	1.00e-12	69
regional part of forebrain	1.95e-12	41
forebrain	1.95e-12	41
future forebrain	1.95e-12	41
anterior neural tube	4.57e-12	42
regional part of brain	1.55e-11	59
telencephalon	1.73e-10	34
gray matter	2.23e-10	34
brain grey matter	2.23e-10	34
regional part of telencephalon	3.99e-10	33
cerebral hemisphere	6.42e-10	32
neurectoderm	2.48e-08	90
regional part of cerebral cortex	5.40e-08	22
neocortex	6.21e-08	20
blood	2.25e-07	15
haemolymphatic fluid	2.25e-07	15
organism substance	2.25e-07	15
neural plate	2.27e-07	86
presumptive neural plate	2.27e-07	86
cerebral cortex	5.42e-07	25
pallium	5.42e-07	25

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
ATF3#467	2	14.9754496840058	0.00576829454079388	0.025951361831049
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461190900002824
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0153850762131369
HSF1#3297	2	109.527111111111	0.000110598401343655	0.00153682629562665
IRF3#3661	2	31.3213014743264	0.00133951467332011	0.00887506013873498
NFYA#4800	2	12.2837204665537	0.00851601140372443	0.0324659140351734
NFYB#4801	2	11.1731955023576	0.0102546713505453	0.0381161513694782
PBX3#5090	2	14.6096751244961	0.00605612247321789	0.0268188337423848
SIX5#147912	2	11.391143570306	0.00987382008142903	0.0370659536136144
SP2#6668	2	17.4356869958964	0.00427356848176974	0.0203116054731751
SREBF1#6720	2	31.3372329603255	0.0013381626513618	0.00887398369074705
STAT1#6772	2	13.8043916647995	0.00677093170844408	0.0287482452515729
TFAP2A#7020	2	11.0124229153633	0.0105499065521556	0.039005299150403

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.