Coexpression cluster:C1743

Full id: C1743_cerebellum_pituitary_pineal_lung_parietal_occipital_CD4

Phase1 CAGE Peaks

Hg19::chr15:57025759..57025811,-	p2@ZNF280D
Hg19::chr15:77197655..77197716,-	p1@SCAPER
Hg19::chr18:34409075..34409100,+	p1@KIAA1328
Hg19::chr2:113033164..113033219,+	p1@ZC3H6
Hg19::chr5:180688105..180688162,-	p1@TRIM52

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:0008270	zinc ion binding	0.00757246536841732
GO:0046914	transition metal ion binding	0.00757246536841732
GO:0043169	cation binding	0.0123098686752955
GO:0046872	metal ion binding	0.0123098686752955
GO:0043167	ion binding	0.0123098686752955

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
lymphocyte	8.36e-11	53
common lymphoid progenitor	8.36e-11	53
lymphoid lineage restricted progenitor cell	1.27e-10	52
leukocyte	6.28e-09	140
mature alpha-beta T cell	3.61e-08	18
alpha-beta T cell	3.61e-08	18
immature T cell	3.61e-08	18
mature T cell	3.61e-08	18
immature alpha-beta T cell	3.61e-08	18
hematopoietic lineage restricted progenitor cell	2.40e-07	124
hematopoietic stem cell	2.57e-07	172
angioblastic mesenchymal cell	2.57e-07	172
nongranular leukocyte	5.65e-07	119
T cell	8.89e-07	25
pro-T cell	8.89e-07	25

Uber Anatomy

Ontology term	p-value	n
adult organism	1.68e-46	115
neural tube	1.05e-26	57
neural rod	1.05e-26	57
future spinal cord	1.05e-26	57
neural keel	1.05e-26	57
central nervous system	5.24e-24	82
regional part of nervous system	8.56e-24	94
nervous system	8.56e-24	94
anterior neural tube	1.33e-22	42
regional part of forebrain	2.79e-22	41
forebrain	2.79e-22	41
future forebrain	2.79e-22	41
brain	3.76e-22	69
future brain	3.76e-22	69
regional part of brain	5.28e-22	59
gray matter	4.28e-18	34
brain grey matter	4.28e-18	34
telencephalon	6.04e-18	34
regional part of telencephalon	1.66e-17	33
neurectoderm	1.69e-17	90
cerebral hemisphere	9.19e-17	32
neural plate	1.19e-16	86
presumptive neural plate	1.19e-16	86
regional part of cerebral cortex	3.71e-13	22
cerebral cortex	8.51e-13	25
pallium	8.51e-13	25
pre-chordal neural plate	1.86e-12	61
neocortex	4.22e-12	20
anterior region of body	4.80e-12	129
craniocervical region	4.80e-12	129
ectoderm	2.71e-11	173
presumptive ectoderm	2.71e-11	173
ectoderm-derived structure	1.36e-10	169
head	2.46e-10	123
nucleus of brain	7.45e-07	9
neural nucleus	7.45e-07	9
basal ganglion	8.00e-07	9
nuclear complex of neuraxis	8.00e-07	9
aggregate regional part of brain	8.00e-07	9
collection of basal ganglia	8.00e-07	9
cerebral subcortex	8.00e-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
BCLAF1#9774	3	12.9915885660731	0.000917803240254255	0.00667649596774494
CCNT2#905	5	6.33620157696263	9.78880505817628e-05	0.00139017271073004
CTCF#10664	4	4.28820509846002	0.00515201558824328	0.0239334292331883
E2F4#1874	4	10.1344482522276	0.000181820150963297	0.00220291354367237
E2F6#1876	4	4.01372458535791	0.00663211823393388	0.0282922880579128
ELF1#1997	5	4.25809795880754	0.000714241693977684	0.00572923873097814
GTF2F1#2962	3	7.64379652605459	0.0042841549641205	0.0203443304823253
HMGN3#9324	4	6.54283817868047	0.0010080127776835	0.0072205656027769
IRF1#3659	4	6.10973100285112	0.00131552526476799	0.00880888267789347
MAX#4149	4	5.1620444072057	0.00252630900948518	0.0139978347202304
MYC#4609	5	5.2222818716094	0.000257394484885061	0.00276421826292143
SETDB1#9869	2	16.1280104712042	0.0058505784665934	0.0262694997623624
SIN3A#25942	4	4.32710778145211	0.00497705285576288	0.0232416017528736
SIX5#147912	3	10.2520292132754	0.00183229106867769	0.0108488376280758
SP1#6667	4	4.55870510251272	0.0040757356578168	0.0194830536601395
SP2#6668	2	10.4614121975379	0.0135319118334714	0.0477791453387849
SRF#6722	3	8.27830695730069	0.00340484607377615	0.0173581333153913
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.013528596715915
TCF7L2#6934	4	8.61614125050988	0.000343896972598245	0.00347318981928132
YY1#7528	5	4.91117074985386	0.0003499314082136	0.0035266318964026
ZNF143#7702	4	10.8007012417823	0.000141522343086319	0.00184409881342383
ZNF263#10127	4	6.57747330960854	0.000987510323790016	0.00709121223228173

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.