Coexpression cluster:C4168

Full id: C4168_optic_substantia_spinal_left_pineal_globus_thalamus

Phase1 CAGE Peaks

Hg19::chr2:198669308..198669328,+	p1@PLCL1
Hg19::chr2:198669338..198669358,+	p2@PLCL1
Hg19::chr2:198669365..198669376,+	p3@PLCL1

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
leukocyte	1.65e-08	136
mature alpha-beta T cell	4.33e-07	18
alpha-beta T cell	4.33e-07	18
immature T cell	4.33e-07	18
mature T cell	4.33e-07	18
immature alpha-beta T cell	4.33e-07	18
myeloid leukocyte	8.22e-07	72

Uber Anatomy

Ontology term	p-value	n
adult organism	1.46e-44	114
neural tube	8.32e-26	56
neural rod	8.32e-26	56
future spinal cord	8.32e-26	56
neural keel	8.32e-26	56
regional part of nervous system	5.88e-24	53
regional part of brain	5.88e-24	53
regional part of forebrain	4.96e-21	41
forebrain	4.96e-21	41
anterior neural tube	4.96e-21	41
future forebrain	4.96e-21	41
central nervous system	6.47e-20	81
brain	1.56e-18	68
future brain	1.56e-18	68
brain grey matter	1.28e-17	34
gray matter	1.28e-17	34
telencephalon	1.69e-17	34
nervous system	1.80e-17	89
neural plate	1.96e-16	82
presumptive neural plate	1.96e-16	82
regional part of telencephalon	2.24e-16	32
cerebral hemisphere	3.19e-16	32
neurectoderm	1.85e-14	86
regional part of cerebral cortex	9.73e-14	22
neocortex	9.07e-13	20
cerebral cortex	1.55e-12	25
pallium	1.55e-12	25
pre-chordal neural plate	2.17e-11	61
structure with developmental contribution from neural crest	4.27e-11	132
ecto-epithelium	5.78e-09	104
lateral plate mesoderm	1.24e-08	203
tube	3.09e-08	192
hematopoietic system	1.57e-07	98
blood island	1.57e-07	98
hemolymphoid system	7.78e-07	108

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	0.0190462838909367
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00661527632498795
CTBP2#1488	3	62.7170003393281	4.049570681927e-06	0.000130013253135498
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326229131568773
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463434599735605
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00763663659457695
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00899262556536842
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154445214741944
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128372284434879
IRF3#3661	3	46.9819522114896	9.63568551583244e-06	0.000253742148156335
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000738703434729602
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.0019996127267354
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00246271235108961
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.00136905682974081
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277439807466035
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247060261164471
SP2#6668	3	26.1535304938446	5.58768218891694e-05	0.000941396902933208

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.