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Coexpression cluster:C2924

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Full id: C2924_Synoviocyte_large_left_vagina_extraskeletal_eye_retina



Phase1 CAGE Peaks

Hg19::chr8:27850112..27850121,-p3@SCARA5
Hg19::chr8:27850157..27850179,-p2@SCARA5
Hg19::chr8:27850180..27850202,-p1@SCARA5
Hg19::chr8:27850333..27850357,-p4@SCARA5


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><br>


Cell Type
Ontology termp-valuen
fat cell4.04e-0915
Uber Anatomy
Ontology termp-valuen
adult organism1.00e-42115
neural tube5.65e-1257
neural rod5.65e-1257
future spinal cord5.65e-1257
neural keel5.65e-1257
neural plate4.62e-1186
presumptive neural plate4.62e-1186
multi-tissue structure4.66e-11347
anatomical cluster9.35e-11286
neurectoderm6.51e-1090
anterior neural tube1.81e-0942
regional part of brain2.75e-0959
regional part of forebrain8.22e-0941
forebrain8.22e-0941
future forebrain8.22e-0941
regional part of cerebral cortex2.93e-0822
anterior region of body6.80e-08129
craniocervical region6.80e-08129
central nervous system8.48e-0882
organ1.27e-07511
neocortex1.78e-0720
anatomical conduit2.72e-07241
brain2.95e-0769
future brain2.95e-0769
telencephalon3.37e-0734
gray matter3.46e-0734
brain grey matter3.46e-0734
multi-cellular organism3.77e-07659
organism subdivision4.61e-07365
head5.27e-07123
organ part6.78e-07219
regional part of telencephalon6.98e-0733


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#promotersEnrichmentp-valueq-value
CTCF#1066445.360256373075030.001211145381643620.00820250389167228
HNF4A#3172423.13229036295373.48990320893214e-060.000115929389706636
HNF4G#3174428.75342252644681.46167379934821e-065.67915736347202e-05
RAD21#5885410.35503389545638.6948481184721e-050.00130078963278199
SMC3#9126415.04493284493281.95092670935632e-050.000439785958554856
ZNF143#7702413.50087655222793.00867915035614e-050.000622224637196128



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.