Coexpression cluster:C1815

Full id: C1815_CD4_cerebellum_cord_CD19_pineal_parietal_pituitary

Phase1 CAGE Peaks

Hg19::chr19:19932513..19932569,-	p1@ZNF506
Hg19::chr19:19976634..19976677,+	p2@ZNF253
Hg19::chr19:20748574..20748599,-	p1@ZNF737
Hg19::chr19:22018966..22019001,-	p1@ZNF43
Hg19::chr4:331578..331615,+	p1@ZNF141

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
4.64055626633526e-10	2.93747211659022e-07	5	390	{ASH2L,391} (Static Module):NA

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:0006355	regulation of transcription, DNA-dependent	0.000846431334884364
GO:0006351	transcription, DNA-dependent	0.000846431334884364
GO:0032774	RNA biosynthetic process	0.000846431334884364
GO:0003677	DNA binding	0.000846431334884364
GO:0045449	regulation of transcription	0.000846431334884364
GO:0005730	nucleolus	0.000846431334884364
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.000846431334884364
GO:0006350	transcription	0.000846431334884364
GO:0010468	regulation of gene expression	0.000846431334884364
GO:0031323	regulation of cellular metabolic process	0.000846431334884364
GO:0019222	regulation of metabolic process	0.000846431334884364
GO:0016070	RNA metabolic process	0.000846431334884364
GO:0008270	zinc ion binding	0.000846431334884364
GO:0046914	transition metal ion binding	0.00151449307368346
GO:0010467	gene expression	0.00216810207862511
GO:0050794	regulation of cellular process	0.00243180912712297
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00252885068474743
GO:0005634	nucleus	0.00274969000691553
GO:0050789	regulation of biological process	0.00274969000691553
GO:0003676	nucleic acid binding	0.00303959206670695
GO:0043169	cation binding	0.00311902856622841
GO:0065007	biological regulation	0.00343002124051222
GO:0046872	metal ion binding	0.00350277187617976
GO:0043167	ion binding	0.00359037836362785
GO:0031981	nuclear lumen	0.0047146401294312
GO:0043283	biopolymer metabolic process	0.00562041980758463
GO:0043231	intracellular membrane-bound organelle	0.00744887228320251
GO:0043227	membrane-bound organelle	0.00744887228320251
GO:0003704	specific RNA polymerase II transcription factor activity	0.00744887228320251
GO:0031974	membrane-enclosed lumen	0.00744887228320251
GO:0043233	organelle lumen	0.00744887228320251
GO:0044428	nuclear part	0.0093458991010516
GO:0043229	intracellular organelle	0.0145414453986348
GO:0043226	organelle	0.0145414453986348
GO:0043170	macromolecule metabolic process	0.016205067423626
GO:0044237	cellular metabolic process	0.026309483769755
GO:0044238	primary metabolic process	0.026383330268527
GO:0044424	intracellular part	0.0272869829045711
GO:0016564	transcription repressor activity	0.0313615375688903
GO:0003702	RNA polymerase II transcription factor activity	0.0397506666735284
GO:0005622	intracellular	0.0442867803553934
GO:0043232	intracellular non-membrane-bound organelle	0.0448997808200877
GO:0043228	non-membrane-bound organelle	0.0448997808200877

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	1.50e-10	52
lymphocyte	8.94e-10	53
common lymphoid progenitor	8.94e-10	53
mature alpha-beta T cell	3.10e-09	18
alpha-beta T cell	3.10e-09	18
immature T cell	3.10e-09	18
mature T cell	3.10e-09	18
immature alpha-beta T cell	3.10e-09	18
nucleate cell	3.31e-09	55
leukocyte	2.23e-07	136
CD8-positive, alpha-beta T cell	3.94e-07	11
B cell	5.11e-07	14

Uber Anatomy

Ontology term	p-value	n
adult organism	9.28e-29	114
nervous system	1.02e-21	89
central nervous system	8.69e-21	81
neural tube	6.64e-20	56
neural rod	6.64e-20	56
future spinal cord	6.64e-20	56
neural keel	6.64e-20	56
regional part of nervous system	1.22e-18	53
regional part of brain	1.22e-18	53
regional part of forebrain	5.00e-17	41
forebrain	5.00e-17	41
anterior neural tube	5.00e-17	41
future forebrain	5.00e-17	41
neurectoderm	6.63e-17	86
brain	7.56e-16	68
future brain	7.56e-16	68
neural plate	9.08e-16	82
presumptive neural plate	9.08e-16	82
brain grey matter	1.71e-13	34
gray matter	1.71e-13	34
telencephalon	2.10e-13	34
pre-chordal neural plate	3.04e-13	61
regional part of telencephalon	7.03e-13	32
cerebral hemisphere	1.29e-12	32
ecto-epithelium	2.83e-11	104
ectoderm-derived structure	2.87e-11	171
ectoderm	2.87e-11	171
presumptive ectoderm	2.87e-11	171
cerebral cortex	8.40e-10	25
pallium	8.40e-10	25
regional part of cerebral cortex	9.86e-10	22
neocortex	7.36e-09	20
structure with developmental contribution from neural crest	2.94e-08	132
blood	7.79e-07	15
haemolymphatic fluid	7.79e-07	15
organism substance	7.79e-07	15

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
CHD2#1106	3	6.20641370047011	0.00777455012627559	0.0319558518886259
ELF1#1997	5	4.25809795880754	0.000714241693977684	0.00573232062378663
FOS#2353	5	8.9979553088944	1.69470025615156e-05	0.000389166227027733
GATA2#2624	4	10.1959453868432	0.000177544777760982	0.00215711947936007
GATA3#2625	3	16.3419098143236	0.000467886519508923	0.00430192800519345
IRF3#3661	3	28.1891713268937	9.33088977565955e-05	0.00135631008668073
NFYA#4800	4	14.7404645598644	4.14733626928016e-05	0.000752246704806096
NFYB#4801	4	13.4078346028292	6.03169250119439e-05	0.00099141317773409
PBX3#5090	3	13.1487076120465	0.000886046932280843	0.00660371480485827
POU2F2#5452	4	7.28489924619402	0.000663122328874386	0.00542587221132184
SP1#6667	5	5.6983813781409	0.00016639184371255	0.00204324488718342
SP2#6668	2	10.4614121975379	0.0135319118334714	0.0477823761698589
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135395830702401
TAF7#6879	4	9.14645552393913	0.000272066287241299	0.00290297619260258
TBP#6908	5	3.70677068709639	0.00142875510672112	0.009189417082821

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.