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Coexpression cluster:C2823: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0045123!cellular extravasation!0.0155415249616414!3672$GO:0030593!neutrophil chemotaxis!0.0223346942055352!3672$GO:0005518!collagen binding!0.0223346942055352!3672$GO:0030595!leukocyte chemotaxis!0.0223346942055352!3672$GO:0050900!leukocyte migration!0.0240797902081608!3672$GO:0009897!external side of plasma membrane!0.0305050789062747!3672$GO:0008305!integrin complex!0.0305050789062747!3672$GO:0007229!integrin-mediated signaling pathway!0.038793191786861!3672$GO:0007160!cell-matrix adhesion!0.038793191786861!3672$GO:0031589!cell-substrate adhesion!0.038793191786861!3672$GO:0043235!receptor complex!0.038793191786861!3672$GO:0042330!taxis!0.0409869718598991!3672$GO:0006935!chemotaxis!0.0409869718598991!3672$GO:0009986!cell surface!0.0409869718598991!3672$GO:0007626!locomotory behavior!0.0467614554761341!3672
|gostat_on_coexpression_clusters=GO:0045123!cellular extravasation!0.0155415249616414!3672$GO:0030593!neutrophil chemotaxis!0.0223346942055352!3672$GO:0005518!collagen binding!0.0223346942055352!3672$GO:0030595!leukocyte chemotaxis!0.0223346942055352!3672$GO:0050900!leukocyte migration!0.0240797902081608!3672$GO:0009897!external side of plasma membrane!0.0305050789062747!3672$GO:0008305!integrin complex!0.0305050789062747!3672$GO:0007229!integrin-mediated signaling pathway!0.038793191786861!3672$GO:0007160!cell-matrix adhesion!0.038793191786861!3672$GO:0031589!cell-substrate adhesion!0.038793191786861!3672$GO:0043235!receptor complex!0.038793191786861!3672$GO:0042330!taxis!0.0409869718598991!3672$GO:0006935!chemotaxis!0.0409869718598991!3672$GO:0009986!cell surface!0.0409869718598991!3672$GO:0007626!locomotory behavior!0.0467614554761341!3672
|id=C2823
|id=C2823
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!1.12e-16!659;UBERON:0000481!1.87e-15!347;UBERON:0000477!4.28e-13!286;UBERON:0000467!1.07e-12!625;UBERON:0000480!2.20e-12!626;UBERON:0003104!2.84e-10!238;UBERON:0009142!2.84e-10!238;UBERON:0000475!4.54e-10!365;UBERON:0007023!4.91e-10!115;UBERON:0005256!2.86e-09!143;UBERON:0000490!1.09e-08!138;UBERON:0000062!2.38e-08!511;UBERON:0002100!8.43e-08!216;UBERON:0001007!1.09e-07!155;UBERON:0001555!1.09e-07!155;UBERON:0007026!1.09e-07!155;UBERON:0000922!1.56e-07!612;UBERON:0002050!1.90e-07!605;UBERON:0005423!1.90e-07!605;UBERON:0000119!2.10e-07!312;UBERON:0002385!2.37e-07!63;UBERON:0001015!2.37e-07!63;UBERON:0000383!2.37e-07!63;UBERON:0000483!2.63e-07!309;UBERON:0001048!3.01e-07!168;UBERON:0000923!3.37e-07!604;UBERON:0005291!3.37e-07!604;UBERON:0006598!3.37e-07!604;UBERON:0002532!3.37e-07!604;UBERON:0004111!4.06e-07!241;UBERON:0004119!4.83e-07!169;UBERON:0000925!4.83e-07!169;UBERON:0006595!4.83e-07!169;UBERON:0001737!6.79e-07!9;UBERON:0004921!7.05e-07!129;UBERON:0004185!7.05e-07!129
}}
}}

Revision as of 14:28, 21 May 2012


Full id: C2823_mesenchymal_alveolar_spleen_Smooth_normal_mesodermal_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr5:52083733..52083821,+p1@ITGA1
p2@PELO
Hg19::chr5:52083828..52083843,+p6@PELO
Hg19::chr5:52083850..52083861,+p9@PELO
Hg19::chr5:52083886..52083895,+p10@PELO


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 IDGO nameFDR corrected p-value
GO:0045123cellular extravasation0.0155415249616414
GO:0030593neutrophil chemotaxis0.0223346942055352
GO:0005518collagen binding0.0223346942055352
GO:0030595leukocyte chemotaxis0.0223346942055352
GO:0050900leukocyte migration0.0240797902081608
GO:0009897external side of plasma membrane0.0305050789062747
GO:0008305integrin complex0.0305050789062747
GO:0007229integrin-mediated signaling pathway0.038793191786861
GO:0007160cell-matrix adhesion0.038793191786861
GO:0031589cell-substrate adhesion0.038793191786861
GO:0043235receptor complex0.038793191786861
GO:0042330taxis0.0409869718598991
GO:0006935chemotaxis0.0409869718598991
GO:0009986cell surface0.0409869718598991
GO:0007626locomotory behavior0.0467614554761341



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>


Uber Anatomy
Ontology termp-valuen
multi-cellular organism1.12e-16659
multi-tissue structure1.87e-15347
anatomical cluster4.28e-13286
anatomical system1.07e-12625
anatomical group2.20e-12626
mesenchyme2.84e-10238
entire embryonic mesenchyme2.84e-10238
organism subdivision4.54e-10365
adult organism4.91e-10115
trunk mesenchyme2.86e-09143
unilaminar epithelium1.09e-08138
organ2.38e-08511
trunk8.43e-08216
digestive system1.09e-07155
digestive tract1.09e-07155
primitive gut1.09e-07155
embryo1.56e-07612
embryonic structure1.90e-07605
developing anatomical structure1.90e-07605
cell layer2.10e-07312
muscle tissue2.37e-0763
musculature2.37e-0763
musculature of body2.37e-0763
epithelium2.63e-07309
primordium3.01e-07168
germ layer3.37e-07604
embryonic tissue3.37e-07604
presumptive structure3.37e-07604
epiblast (generic)3.37e-07604
anatomical conduit4.06e-07241
endoderm-derived structure4.83e-07169
endoderm4.83e-07169
presumptive endoderm4.83e-07169
larynx6.79e-079
subdivision of digestive tract7.05e-07129
endodermal part of digestive tract7.05e-07129


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.