Coexpression cluster:C3394

Full id: C3394_Eosinophils_CD14_cerebellum_pineal_Neutrophils_CD4_Peripheral

Phase1 CAGE Peaks

Hg19::chr14:102414651..102414721,+	p@chr14:102414651..102414721 +
Hg19::chr2:157198916..157198978,-	p2@NR4A2
Hg19::chr5:98264867..98264903,+	p1@ENST00000513175

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:0042053	regulation of dopamine metabolic process	0.00500412104085718
GO:0042069	regulation of catecholamine metabolic process	0.00500412104085718
GO:0042417	dopamine metabolic process	0.00917422190823815
GO:0006584	catecholamine metabolic process	0.0133443227756191
GO:0018958	phenol metabolic process	0.0133443227756191
GO:0042133	neurotransmitter metabolic process	0.0133443227756191
GO:0006576	biogenic amine metabolic process	0.0243950900741787
GO:0001505	regulation of neurotransmitter levels	0.0243950900741787
GO:0006575	amino acid derivative metabolic process	0.0250206052042859
GO:0003707	steroid hormone receptor activity	0.0292741080890145
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0316169465763249
GO:0004879	ligand-dependent nuclear receptor activity	0.0319012716354645
GO:0006725	aromatic compound metabolic process	0.0352213134798794
GO:0030182	neuron differentiation	0.0362798775462145
GO:0045893	positive regulation of transcription, DNA-dependent	0.0362798775462145
GO:0048699	generation of neurons	0.0362798775462145
GO:0022008	neurogenesis	0.0362798775462145
GO:0045941	positive regulation of transcription	0.0362798775462145
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0362798775462145
GO:0007268	synaptic transmission	0.0362798775462145
GO:0019226	transmission of nerve impulse	0.0393180938924492
GO:0031325	positive regulation of cellular metabolic process	0.0415114586343834
GO:0009893	positive regulation of metabolic process	0.042535028847286
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.0440988166725538
GO:0006066	alcohol metabolic process	0.0445366772636289

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	2.58e-27	140
CD14-positive, CD16-negative classical monocyte	4.21e-25	42
myeloid leukocyte	5.30e-24	76
classical monocyte	6.17e-24	45
hematopoietic lineage restricted progenitor cell	2.83e-23	124
nongranular leukocyte	2.88e-21	119
myeloid lineage restricted progenitor cell	8.96e-20	70
hematopoietic stem cell	1.98e-19	172
angioblastic mesenchymal cell	1.98e-19	172
granulocyte monocyte progenitor cell	2.18e-19	71
hematopoietic cell	1.30e-18	182
macrophage dendritic cell progenitor	2.13e-18	65
hematopoietic oligopotent progenitor cell	7.89e-18	165
hematopoietic multipotent progenitor cell	7.89e-18	165
monopoietic cell	1.06e-17	63
monocyte	1.06e-17	63
monoblast	1.06e-17	63
promonocyte	1.06e-17	63
myeloid cell	1.01e-13	112
common myeloid progenitor	1.01e-13	112
intermediate monocyte	6.84e-07	9
CD14-positive, CD16-positive monocyte	6.84e-07	9
mature alpha-beta T cell	7.59e-07	18
alpha-beta T cell	7.59e-07	18
immature T cell	7.59e-07	18
mature T cell	7.59e-07	18
immature alpha-beta T cell	7.59e-07	18

Uber Anatomy

Ontology term	p-value	n
adult organism	1.09e-28	115
hematopoietic system	3.12e-22	102
blood island	3.12e-22	102
neural tube	6.78e-20	57
neural rod	6.78e-20	57
future spinal cord	6.78e-20	57
neural keel	6.78e-20	57
bone marrow	1.30e-19	80
hemolymphoid system	7.14e-19	112
bone element	1.83e-18	86
regional part of brain	4.07e-16	59
anterior neural tube	1.10e-15	42
regional part of forebrain	2.07e-15	41
forebrain	2.07e-15	41
future forebrain	2.07e-15	41
skeletal element	3.99e-15	101
skeletal system	3.99e-15	101
brain	8.47e-13	69
future brain	8.47e-13	69
gray matter	2.41e-12	34
brain grey matter	2.41e-12	34
telencephalon	4.38e-12	34
regional part of telencephalon	7.49e-12	33
cerebral hemisphere	2.81e-11	32
central nervous system	3.48e-11	82
immune system	1.89e-10	115
neural plate	7.89e-10	86
presumptive neural plate	7.89e-10	86
regional part of cerebral cortex	2.47e-09	22
neurectoderm	3.79e-09	90
cerebral cortex	1.19e-08	25
pallium	1.19e-08	25
regional part of nervous system	1.44e-08	94
nervous system	1.44e-08	94
neocortex	1.73e-08	20
pre-chordal neural plate	3.58e-07	61

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189557003733319
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324253944180366
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321170027037718
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460908037927042
GTF2B#2959	2	21.2958866228828	0.00287818058991141	0.0155756413611978
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108491134795504
HNF4A#3172	2	15.4215269086358	0.00544421048668661	0.0246729398576291
MEF2A#4205	2	12.495487273096	0.00823502947802974	0.032479540923563
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00470161469991909
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172577869050448
SREBF2#6721	1	145.647754137116	0.00685021551456999	0.0290447246722221
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00541556282756503
TFAP2A#7020	2	11.0124229153633	0.0105499065521556	0.0390011571413608
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328508087507215

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.