Coexpression cluster:C1843

Full id: C1843_signet_lung_cord_bile_colon_retina_adenocarcinoma

Phase1 CAGE Peaks

Hg19::chr1:205905161..205905166,-	p5@SLC26A9
Hg19::chr7:129008057..129008070,+	p10@AHCYL2
Hg19::chr7:129008104..129008114,+	p15@AHCYL2
Hg19::chr7:129008147..129008158,+	p7@AHCYL2
Hg19::chr7:129008160..129008180,+	p5@AHCYL2

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:0015116	sulfate transmembrane transporter activity	0.00582832921229247
GO:0008271	secondary active sulfate transmembrane transporter activity	0.00582832921229247
GO:0008272	sulfate transport	0.00582832921229247
GO:0015103	inorganic anion transmembrane transporter activity	0.0114947603909102
GO:0008509	anion transmembrane transporter activity	0.027069351230425
GO:0015698	inorganic anion transport	0.0280623258369638
GO:0006820	anion transport	0.0291416460614624
GO:0015291	secondary active transmembrane transporter activity	0.0291416460614624
GO:0022804	active transmembrane transporter activity	0.0481376820126379

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	4.53e-15	114
neural tube	1.58e-12	56
neural rod	1.58e-12	56
future spinal cord	1.58e-12	56
neural keel	1.58e-12	56
regional part of nervous system	6.24e-12	53
regional part of brain	6.24e-12	53
central nervous system	5.40e-10	81
nervous system	2.33e-09	89
neurectoderm	2.53e-09	86
brain	3.94e-09	68
future brain	3.94e-09	68
neural plate	5.60e-09	82
presumptive neural plate	5.60e-09	82
regional part of forebrain	1.39e-08	41
forebrain	1.39e-08	41
anterior neural tube	1.39e-08	41
future forebrain	1.39e-08	41
medulla oblongata	1.49e-08	3
myelencephalon	1.49e-08	3
future myelencephalon	1.49e-08	3
telencephalon	9.05e-08	34
organ system subdivision	1.16e-07	223
brainstem	5.15e-07	6

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
BATF#10538	4	19.4862414338429	1.37275300118359e-05	0.000332257127904086
CEBPB#1051	4	6.37691810065985	0.00111394417667732	0.00765540671632573
EBF1#1879	4	7.1251734772552	0.000723053104677421	0.00577198984937745
EP300#2033	4	5.41915338097856	0.0020938692794389	0.0121186818329354
FOXA1#3169	4	8.86513579950836	0.000307546859137271	0.00316764165891888
GATA3#2625	4	21.7892130857648	8.81158303710445e-06	0.000237612424686845
HDAC2#3066	4	10.732496189301	0.000145096579747875	0.00188620135577399
NFKB1#4790	4	4.39045073935507	0.00470773269252496	0.022206354486004
SMARCC2#6601	4	75.3242995415181	6.28893529700036e-08	3.88415206081266e-06
SPI1#6688	4	6.56345880681818	0.000995742963645402	0.00714296307302439
STAT1#6772	4	16.5652699977594	2.61308619905866e-05	0.000564092826671118

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.