Coexpression cluster:C3989

Full id: C3989_pineal_pituitary_optic_spinal_corpus_substantia_thalamus

Phase1 CAGE Peaks

Hg19::chr1:61542891..61542920,+	p12@NFIA
Hg19::chr3:101405675..101405733,+	p@chr3:101405675..101405733 +
Hg19::chr7:7606626..7606650,-	p@chr7:7606626..7606650 -

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
nucleate cell	4.26e-11	55
lymphocyte	8.85e-11	53
common lymphoid progenitor	8.85e-11	53
lymphoid lineage restricted progenitor cell	9.87e-11	52
leukocyte	4.28e-08	136
hematopoietic lineage restricted progenitor cell	5.26e-08	120
mature alpha-beta T cell	1.55e-07	18
alpha-beta T cell	1.55e-07	18
immature T cell	1.55e-07	18
mature T cell	1.55e-07	18
immature alpha-beta T cell	1.55e-07	18
nongranular leukocyte	2.99e-07	115
T cell	8.65e-07	25
pro-T cell	8.65e-07	25

Uber Anatomy

Ontology term	p-value	n
adult organism	1.58e-41	114
neural tube	8.73e-28	56
neural rod	8.73e-28	56
future spinal cord	8.73e-28	56
neural keel	8.73e-28	56
nervous system	1.83e-27	89
central nervous system	2.01e-26	81
regional part of nervous system	5.50e-26	53
regional part of brain	5.50e-26	53
brain	6.97e-24	68
future brain	6.97e-24	68
regional part of forebrain	1.52e-23	41
forebrain	1.52e-23	41
anterior neural tube	1.52e-23	41
future forebrain	1.52e-23	41
telencephalon	3.52e-19	34
brain grey matter	3.65e-19	34
gray matter	3.65e-19	34
neural plate	5.72e-18	82
presumptive neural plate	5.72e-18	82
regional part of telencephalon	6.77e-18	32
neurectoderm	7.80e-18	86
cerebral hemisphere	8.05e-18	32
pre-chordal neural plate	3.34e-14	61
regional part of cerebral cortex	8.92e-14	22
cerebral cortex	1.55e-13	25
pallium	1.55e-13	25
neocortex	8.86e-13	20
organ system subdivision	9.40e-13	223
ecto-epithelium	5.28e-11	104
ectoderm-derived structure	6.84e-10	171
ectoderm	6.84e-10	171
presumptive ectoderm	6.84e-10	171
neural nucleus	3.51e-07	9
nucleus of brain	3.51e-07	9
basal ganglion	3.80e-07	9
nuclear complex of neuraxis	3.80e-07	9
aggregate regional part of brain	3.80e-07	9
collection of basal ganglia	3.80e-07	9
cerebral subcortex	3.80e-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
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325736084001893
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.046283203644299
ELK4#2005	2	10.823787772312	0.0109128471951648	0.0401977514977538
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154268006296949
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294856804329156
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.026982335573147
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277125249861198
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246811763941102
TFAP2A#7020	2	11.0124229153633	0.0105499065521556	0.0390204940468386
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00616291812481426
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190515364171373
ZZZ3#26009	1	79.8044041450777	0.012478437908258	0.0451634175457636

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.