Coexpression cluster:C85: Difference between revisions
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|id=C85 | |id=C85 | ||
|ontology_enrichment_celltype= | |ontology_enrichment_celltype= | ||
|ontology_enrichment_disease= | |ontology_enrichment_disease=DOID:169!4.27e-34!6;DOID:171!3.81e-21!10;DOID:3095!1.80e-10!22;DOID:2994!1.80e-10!22 | ||
|ontology_enrichment_uberon=UBERON:0000013!1.48e-40!5;UBERON:0002410!1.48e-40!5;UBERON:0000010!2.62e-23!8 | |||
|tf_chipseq_enrich=CTBP2#1488;10:2.8769266210701:0.00286843567574545:0.0155406211308388!GATA2#2624;29:1.6954266985003:0.00375252859097994:0.0186739569025279!NANOG#79923;15:2.01225540006968:0.00852502610532537:0.0324931645346548!SUZ12#23512;16:3.6782224521881:9.8197633091822e-06:0.000257615237439759 | |tf_chipseq_enrich=CTBP2#1488;10:2.8769266210701:0.00286843567574545:0.0155406211308388!GATA2#2624;29:1.6954266985003:0.00375252859097994:0.0186739569025279!NANOG#79923;15:2.01225540006968:0.00852502610532537:0.0324931645346548!SUZ12#23512;16:3.6782224521881:9.8197633091822e-06:0.000257615237439759 | ||
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| ||
}} | }} |
Revision as of 16:47, 19 October 2012
Full id: C85_neuroblastoma_carcinoid_retinoblastoma_small_pineal_rhabdomyosarcoma_medulloblastoma
Phase1 CAGE Peaks
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
GO ID | GO name | FDR corrected p-value |
---|---|---|
GO:0007399 | nervous system development | 0.000171765853094219 |
GO:0048731 | system development | 0.0017186126688088 |
GO:0007275 | multicellular organismal development | 0.00189814892299092 |
GO:0032502 | developmental process | 0.00343797603353163 |
GO:0048856 | anatomical structure development | 0.00343797603353163 |
GO:0032501 | multicellular organismal process | 0.00780958209236935 |
GO:0010468 | regulation of gene expression | 0.00780958209236935 |
GO:0031323 | regulation of cellular metabolic process | 0.00848662852663684 |
GO:0019222 | regulation of metabolic process | 0.0118067418075942 |
GO:0005737 | cytoplasm | 0.0143010395208181 |
GO:0045449 | regulation of transcription | 0.0164689418232576 |
GO:0007417 | central nervous system development | 0.0164689418232576 |
GO:0019219 | regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0164689418232576 |
GO:0007501 | mesodermal cell fate specification | 0.0164689418232576 |
GO:0043231 | intracellular membrane-bound organelle | 0.0164689418232576 |
GO:0043227 | membrane-bound organelle | 0.0164689418232576 |
GO:0006350 | transcription | 0.0164689418232576 |
GO:0050794 | regulation of cellular process | 0.018115554288896 |
GO:0045165 | cell fate commitment | 0.0222460872433 |
GO:0048869 | cellular developmental process | 0.0222460872433 |
GO:0030154 | cell differentiation | 0.0222460872433 |
GO:0016070 | RNA metabolic process | 0.0222460872433 |
GO:0016167 | glial cell line-derived neurotrophic factor receptor activity | 0.0222460872433 |
GO:0050774 | negative regulation of dendrite morphogenesis | 0.0222460872433 |
GO:0006355 | regulation of transcription, DNA-dependent | 0.0235101997012121 |
GO:0050789 | regulation of biological process | 0.0236139168726967 |
GO:0006351 | transcription, DNA-dependent | 0.0247288604075228 |
GO:0032774 | RNA biosynthetic process | 0.0247288604075228 |
GO:0044424 | intracellular part | 0.0262669635116243 |
GO:0048814 | regulation of dendrite morphogenesis | 0.0266862685324948 |
GO:0043229 | intracellular organelle | 0.0286528967531669 |
GO:0043226 | organelle | 0.0286528967531669 |
GO:0010467 | gene expression | 0.0286528967531669 |
GO:0008266 | poly(U) binding | 0.0296413736381096 |
GO:0050773 | regulation of dendrite development | 0.0296413736381096 |
GO:0048813 | dendrite morphogenesis | 0.0296413736381096 |
GO:0005783 | endoplasmic reticulum | 0.0310095440878635 |
GO:0065007 | biological regulation | 0.0310095440878635 |
GO:0001537 | N-acetylgalactosamine 4-O-sulfotransferase activity | 0.0310095440878635 |
GO:0006911 | phagocytosis, engulfment | 0.0310095440878635 |
GO:0004994 | somatostatin receptor activity | 0.0310095440878635 |
GO:0003923 | GPI-anchor transamidase activity | 0.0310095440878635 |
GO:0016255 | attachment of GPI anchor to protein | 0.0310095440878635 |
GO:0007617 | mating behavior | 0.0348760096553614 |
GO:0019098 | reproductive behavior | 0.0348760096553614 |
GO:0006139 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0348760096553614 |
GO:0005515 | protein binding | 0.0363028831603493 |
GO:0001710 | mesodermal cell fate commitment | 0.0374235450638049 |
GO:0048333 | mesodermal cell differentiation | 0.0374235450638049 |
GO:0045211 | postsynaptic membrane | 0.0374235450638049 |
GO:0042765 | GPI-anchor transamidase complex | 0.0417900332832 |
GO:0044456 | synapse part | 0.0418186566332716 |
GO:0004459 | L-lactate dehydrogenase activity | 0.0435798547184848 |
GO:0019642 | anaerobic glycolysis | 0.0435798547184848 |
GO:0005844 | polysome | 0.0435798547184848 |
GO:0004457 | lactate dehydrogenase activity | 0.0475412938402424 |
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>disease_data<br>
Ontology term | p-value | n |
---|---|---|
sympathetic nervous system | 1.48e-40 | 5 |
autonomic nervous system | 1.48e-40 | 5 |
peripheral nervous system | 2.62e-23 | 8 |
Ontology term | p-value | n |
---|---|---|
neuroendocrine tumor | 4.27e-34 | 6 |
neuroectodermal tumor | 3.81e-21 | 10 |
germ cell and embryonal cancer | 1.80e-10 | 22 |
germ cell cancer | 1.80e-10 | 22 |
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
(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)
TF | #promoters | Enrichment | p-value | q-value |
---|---|---|---|---|
CTBP2#1488 | 10 | 2.8769266210701 | 0.00286843567574545 | 0.0155406211308388 |
GATA2#2624 | 29 | 1.6954266985003 | 0.00375252859097994 | 0.0186739569025279 |
NANOG#79923 | 15 | 2.01225540006968 | 0.00852502610532537 | 0.0324931645346548 |
SUZ12#23512 | 16 | 3.6782224521881 | 9.8197633091822e-06 | 0.000257615237439759 |
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