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Coexpression cluster:C2300: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0003937!1.61e-37!12;UBERON:0005399!1.61e-37!12;UBERON:0000162!1.16e-31!14;UBERON:0001353!1.16e-31!14;UBERON:0000163!1.16e-31!14;UBERON:0006866!1.16e-31!14;UBERON:0000164!1.16e-31!14;UBERON:0000931!1.16e-31!14;UBERON:0002367!2.25e-31!11;UBERON:0010147!2.25e-31!11;UBERON:0009846!2.25e-31!11;UBERON:0003353!2.25e-31!11;UBERON:0004902!2.25e-31!11;UBERON:0003820!2.25e-31!11;UBERON:0009847!2.25e-31!11;UBERON:0004122!1.75e-29!15;UBERON:0003101!2.22e-25!22;UBERON:0000079!2.22e-25!22;UBERON:0003064!4.00e-24!28;UBERON:0001046!4.65e-23!19;UBERON:0000077!1.41e-18!29;UBERON:0005156!3.05e-18!59;UBERON:0000990!3.05e-18!59;UBERON:0002530!2.42e-15!59;UBERON:0003929!4.04e-14!54;UBERON:0006554!1.35e-13!47;UBERON:0001008!2.80e-13!48;UBERON:0000161!1.17e-11!36;UBERON:0005256!2.51e-10!122;UBERON:0000989!7.01e-09!1;UBERON:0008811!7.01e-09!1;UBERON:0006258!7.01e-09!1;UBERON:0005876!7.01e-09!1;UBERON:0004874!7.01e-09!1;UBERON:0000998!8.15e-09!1;UBERON:0006868!8.15e-09!1;UBERON:0005153!9.03e-09!37;UBERON:0005911!1.20e-08!82;UBERON:0006834!1.37e-08!1;UBERON:0001282!3.28e-08!1;UBERON:0009842!3.28e-08!1;UBERON:0003704!3.28e-08!1;UBERON:0001171!3.28e-08!1;UBERON:0001172!3.28e-08!1;UBERON:0005795!5.43e-08!22;UBERON:0004921!1.07e-07!118;UBERON:0003104!3.32e-07!160;UBERON:0009142!3.32e-07!160;UBERON:0004175!4.92e-07!25;UBERON:0005157!9.95e-07!47
|ontology_enrichment_uberon=UBERON:0003937!1.61e-37!12;UBERON:0005399!1.61e-37!12;UBERON:0000162!1.16e-31!14;UBERON:0001353!1.16e-31!14;UBERON:0000163!1.16e-31!14;UBERON:0006866!1.16e-31!14;UBERON:0000164!1.16e-31!14;UBERON:0000931!1.16e-31!14;UBERON:0002367!2.25e-31!11;UBERON:0010147!2.25e-31!11;UBERON:0009846!2.25e-31!11;UBERON:0003353!2.25e-31!11;UBERON:0004902!2.25e-31!11;UBERON:0003820!2.25e-31!11;UBERON:0009847!2.25e-31!11;UBERON:0004122!1.75e-29!15;UBERON:0003101!2.22e-25!22;UBERON:0000079!2.22e-25!22;UBERON:0003064!4.00e-24!28;UBERON:0001046!4.65e-23!19;UBERON:0000077!1.41e-18!29;UBERON:0005156!3.05e-18!59;UBERON:0000990!3.05e-18!59;UBERON:0002530!2.42e-15!59;UBERON:0003929!4.04e-14!54;UBERON:0006554!1.35e-13!47;UBERON:0001008!2.80e-13!48;UBERON:0000161!1.17e-11!36;UBERON:0005256!2.51e-10!122;UBERON:0000989!7.01e-09!1;UBERON:0008811!7.01e-09!1;UBERON:0006258!7.01e-09!1;UBERON:0005876!7.01e-09!1;UBERON:0004874!7.01e-09!1;UBERON:0000998!8.15e-09!1;UBERON:0006868!8.15e-09!1;UBERON:0005153!9.03e-09!37;UBERON:0005911!1.20e-08!82;UBERON:0006834!1.37e-08!1;UBERON:0001282!3.28e-08!1;UBERON:0009842!3.28e-08!1;UBERON:0003704!3.28e-08!1;UBERON:0001171!3.28e-08!1;UBERON:0001172!3.28e-08!1;UBERON:0005795!5.43e-08!22;UBERON:0004921!1.07e-07!118;UBERON:0003104!3.32e-07!160;UBERON:0009142!3.32e-07!160;UBERON:0004175!4.92e-07!25;UBERON:0005157!9.95e-07!47
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}}
}}

Revision as of 15:24, 26 November 2012


Full id: C2300_tridermal_sacrococcigeal_hepatic_granulosa_penis_normal_glioblastoma



Phase1 CAGE Peaks

Hg19::chr14:53968294..53968300,-p@chr14:53968294..53968300
-
Hg19::chr2:217537503..217537532,-p28@IGFBP5
Hg19::chr7:105865829..105865838,-p@chr7:105865829..105865838
-
Hg19::chr7:27242115..27242139,+p@chr7:27242115..27242139
+


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

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

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>disease_data<br>

Cell Type
Ontology termp-valuen
prostate stromal cell1.96e-223
smooth muscle cell of prostate1.00e-152
Uber Anatomy
Ontology termp-valuen
sex gland1.61e-3712
male reproductive gland1.61e-3712
cloaca1.16e-3114
anal region1.16e-3114
embryonic cloaca1.16e-3114
terminal part of digestive tract1.16e-3114
primitive urogenital sinus1.16e-3114
proctodeum1.16e-3114
prostate gland2.25e-3111
male accessory sex gland2.25e-3111
embryonic cloacal epithelium2.25e-3111
epithelium of hindgut2.25e-3111
urogenital sinus epithelium2.25e-3111
prostate bud2.25e-3111
prostate field2.25e-3111
genitourinary system1.75e-2915
male organism2.22e-2522
male reproductive system2.22e-2522
intermediate mesoderm4.00e-2428
hindgut4.65e-2319
mixed endoderm/mesoderm-derived structure1.41e-1829
reproductive structure3.05e-1859
reproductive system3.05e-1859
gland2.42e-1559
gut epithelium4.04e-1454
urinary system structure1.35e-1347
renal system2.80e-1348
orifice1.17e-1136
trunk mesenchyme2.51e-10122
penis7.01e-091
intromittent organ7.01e-091
lateral plate mesenchyme7.01e-091
undifferentiated genital tubercle7.01e-091
somatopleure7.01e-091
seminal vesicle8.15e-091
seminal fluid secreting gland8.15e-091
epithelial bud9.03e-0937
endo-epithelium1.20e-0882
uterus or analog1.37e-081
intralobular bile duct3.28e-081
acinus3.28e-081
intrahepatic bile duct3.28e-081
portal lobule3.28e-081
hepatic acinus3.28e-081
embryonic uterus5.43e-0822
subdivision of digestive tract1.07e-07118
mesenchyme3.32e-07160
entire embryonic mesenchyme3.32e-07160
internal genitalia4.92e-0725
epithelial fold9.95e-0747
Disease
Ontology termp-valuen
teratoma3.30e-162
pleomorphic carcinoma1.48e-081


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

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

No analysis results for this cluster

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

This analysis result is provided for C0 - C305 clusters.

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