Coexpression cluster:C1872: Difference between revisions

Revision as of 15:09, 26 November 2012

Full id: C1872_signet_Melanocyte_large_parotid_submaxillary_salivary_retina

Phase1 CAGE Peaks

Hg19::chr20:61297992..61297993,-	p2@ENST00000451648
Hg19::chr20:61297994..61298009,-	p1@ENST00000451648
Hg19::chr20:61298021..61298038,-	p1@ENST00000411824
Hg19::chr20:61298923..61298943,+	p3@SLCO4A1
Hg19::chr20:61298969..61298988,+	p6@SLCO4A1

Enriched pathways on this co-expression clusterSummary: 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. Analyst: Emmanuel Dimont link to source dataset data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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. Analyst: Erik Arner link to source dataset data

GO ID	GO name	FDR corrected p-value
GO:0015349	thyroid hormone transmembrane transporter activity	0.00129518426939833
GO:0042403	thyroid hormone metabolic process	0.00388555280819498
GO:0006576	biogenic amine metabolic process	0.0116566584245849
GO:0042445	hormone metabolic process	0.0116566584245849
GO:0006575	amino acid derivative metabolic process	0.0116566584245849
GO:0015291	secondary active transmembrane transporter activity	0.0388555280819498
GO:0006519	amino acid and derivative metabolic process	0.0439067467326033
GO:0009308	amine metabolic process	0.0439067467326033
GO:0022804	active transmembrane transporter activity	0.0439067467326033
GO:0006807	nitrogen compound metabolic process	0.0439067467326033

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji links to source dataset cell_data uberon_data disease_data

Cell Type
Ontology term	p-value	n
melanocyte	1.13e-30	10
melanoblast	1.13e-30	10
pigment cell	1.15e-21	14
light melanocyte	5.41e-20	3
neurecto-epithelial cell	6.71e-15	20
columnar/cuboidal epithelial cell	8.46e-11	27
epithelial cell of stomach	1.90e-09	3
ecto-epithelial cell	2.19e-08	34
dark melanocyte	8.54e-08	1

Uber Anatomy
Ontology term	p-value	n
major salivary gland	1.71e-13	2
open tracheal system trachea	5.53e-13	2
saliva-secreting gland	6.64e-10	6
gland of oral region	6.64e-10	6
gland of foregut	6.64e-10	6
oral gland	6.64e-10	6
oral cavity	6.64e-10	6
pons	1.13e-08	3
parotid gland	1.25e-07	1
cheek	1.25e-07	1
parotid gland primordium	1.25e-07	1
submandibular gland	1.51e-07	1
submandibular gland primordium	1.51e-07	1
tonsil	4.90e-07	1
mucosa-associated lymphoid tissue	4.90e-07	1
lymphoid tissue	4.90e-07	1
tonsillar ring	4.90e-07	1

Disease
Ontology term	p-value	n
signet ring cell adenocarcinoma	1.71e-13	2

Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon link to source data Novel motifs data Jaspar motifs data

Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysisSummary: 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. Analyst: Erik Arner link to source dataset data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
ESR1#2099	3	18.4611619776927	0.00032663345909756	0.00333039849992093
RAD21#5885	3	6.2130203372738	0.00775105506881164	0.031896940002822
USF1#7391	5	6.36149927720796	9.59569864925045e-05	0.00136945227005885
USF2#7392	3	7.79531843104175	0.00404892766172205	0.0193770772149837

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. Analyst:NA link to data source data

This analysis result is provided for C0 - C305 clusters.

@@ Line 9: / Line 9: @@
 |tf_chipseq_enrich=ESR1#2099;3:18.4611619776927:0.00032663345909756:0.00333039849992093!RAD21#5885;3:6.2130203372738:0.00775105506881164:0.031896940002822!USF1#7391;5:6.36149927720796:9.59569864925045e-05:0.00136945227005885!USF2#7392;3:7.79531843104175:0.00404892766172205:0.0193770772149837
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+|tfbs_overrepresentation_for_novel_motifs=0.508327,1.20042,0.500341,0.654974,0.454983,0.653236,0.733342,4.2474,0.859849,0.106358,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.501863,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.700122,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,1.0713,0.432883,0.413782,0.654459,1.78381,0.301779,0.415749,0.580638,0.821929,0.451846,0.0606304,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,0.746838,1.06581,1.08035,1.2359,0.724351,1.17039,0.689906,0.233662,0.688844,1.04369,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,1.23387,0.741483,0.255232,1.25519,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.251545,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.96134,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,1.49565,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,2.58839,1.37132,0.412056,1.00558,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,2.65061,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,1.7291,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,1.69829,3.84951,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,1.12014,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0938701
 }}

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Coexpression cluster:C1872: Difference between revisions

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Revision as of 15:09, 26 November 2012

Phase1 CAGE Peaks

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