Coexpression cluster:C2970

Full id: C2970_optic_corpus_spinal_thalamus_thyroid_diencephalon_globus

Phase1 CAGE Peaks

Hg19::chr10:102133271..102133305,+	p4@LINC00263
Hg19::chr4:42659057..42659100,-	p2@ATP8A1
Hg19::chr4:42659102..42659161,-	p1@ATP8A1

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:0015917	aminophospholipid transport	0.00476863299187566
GO:0004012	phospholipid-translocating ATPase activity	0.00874249381843871
GO:0015247	aminophospholipid transporter activity	0.00874249381843871
GO:0015914	phospholipid transport	0.00874249381843871
GO:0005548	phospholipid transporter activity	0.0101730837160014
GO:0019829	cation-transporting ATPase activity	0.0217994651057173
GO:0005319	lipid transporter activity	0.0217994651057173
GO:0006869	lipid transport	0.0256093253267397
GO:0015662	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism	0.0256093253267397
GO:0042625	ATPase activity, coupled to transmembrane movement of ions	0.0321087954786294
GO:0042626	ATPase activity, coupled to transmembrane movement of substances	0.0321087954786294
GO:0043492	ATPase activity, coupled to movement of substances	0.0321087954786294
GO:0016820	hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances	0.0321087954786294
GO:0015405	P-P-bond-hydrolysis-driven transmembrane transporter activity	0.0321087954786294
GO:0015399	primary active transmembrane transporter activity	0.0321087954786294
GO:0031410	cytoplasmic vesicle	0.0394736842105263
GO:0031982	vesicle	0.0394736842105263
GO:0000287	magnesium ion binding	0.0394736842105263
GO:0042623	ATPase activity, coupled	0.0441726003457956
GO:0016887	ATPase activity	0.0499911691981632

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	3.73e-23	140
hematopoietic stem cell	5.04e-23	172
angioblastic mesenchymal cell	5.04e-23	172
hematopoietic cell	5.86e-22	182
hematopoietic oligopotent progenitor cell	1.48e-20	165
hematopoietic multipotent progenitor cell	1.48e-20	165
lymphocyte	2.77e-20	53
common lymphoid progenitor	2.77e-20	53
lymphoid lineage restricted progenitor cell	5.51e-20	52
nongranular leukocyte	3.65e-19	119
hematopoietic lineage restricted progenitor cell	4.42e-18	124
lymphocyte of B lineage	4.42e-10	24
pro-B cell	4.42e-10	24
T cell	6.71e-10	25
pro-T cell	6.71e-10	25
mature alpha-beta T cell	3.46e-09	18
alpha-beta T cell	3.46e-09	18
immature T cell	3.46e-09	18
mature T cell	3.46e-09	18
immature alpha-beta T cell	3.46e-09	18
B cell	2.10e-07	14

Uber Anatomy

Ontology term	p-value	n
adult organism	5.98e-43	115
neural tube	9.91e-28	57
neural rod	9.91e-28	57
future spinal cord	9.91e-28	57
neural keel	9.91e-28	57
central nervous system	4.37e-23	82
anterior neural tube	6.37e-23	42
regional part of forebrain	7.54e-23	41
forebrain	7.54e-23	41
future forebrain	7.54e-23	41
regional part of nervous system	1.80e-22	94
nervous system	1.80e-22	94
regional part of brain	5.84e-21	59
brain	1.56e-20	69
future brain	1.56e-20	69
neural plate	3.75e-20	86
presumptive neural plate	3.75e-20	86
telencephalon	4.68e-19	34
gray matter	5.74e-19	34
brain grey matter	5.74e-19	34
neurectoderm	6.30e-19	90
regional part of telencephalon	1.83e-18	33
cerebral hemisphere	1.06e-17	32
pre-chordal neural plate	1.21e-15	61
regional part of cerebral cortex	4.08e-14	22
cerebral cortex	2.02e-13	25
pallium	2.02e-13	25
neocortex	5.84e-13	20
anterior region of body	1.37e-09	129
craniocervical region	1.37e-09	129
head	6.95e-08	123
hematopoietic system	1.49e-07	102
blood island	1.49e-07	102
hemolymphoid system	2.16e-07	112
nucleus of brain	4.26e-07	9
neural nucleus	4.26e-07	9
basal ganglion	6.90e-07	9
nuclear complex of neuraxis	6.90e-07	9
aggregate regional part of brain	6.90e-07	9
collection of basal ganglia	6.90e-07	9
cerebral subcortex	6.90e-07	9

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
BRCA1#672	2	13.4561537621492	0.00711980771608456	0.02960605184186
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0188998482107292
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323269379433084
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00912323326450542
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0318825192141332
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0459686301131069
EP300#2033	3	6.7739417262232	0.00321688050010379	0.016674166586448
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00579191684192719
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127527316452688
SIX5#147912	2	11.391143570306	0.00987382008142903	0.037053966779891
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245277905521129
SREBF2#6721	1	145.647754137116	0.00685021551456999	0.0290423665716561
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189385738546939
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0139539768381044
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0108865141979358

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.