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Coexpression cluster:C4833

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Full id: C4833_lung_corpus_thalamus_optic_substantia_globus_diencephalon



Phase1 CAGE Peaks

Hg19::chr9:8857841..8857878,-p1@PTPRD
Hg19::chr9:8857883..8857892,-p14@PTPRD
Hg19::chr9:8857895..8857904,-p13@PTPRD


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism3.71e-34115
neural tube7.40e-3357
neural rod7.40e-3357
future spinal cord7.40e-3357
neural keel7.40e-3357
neural plate3.59e-3286
presumptive neural plate3.59e-3286
central nervous system1.00e-3182
neurectoderm6.04e-2990
regional part of nervous system9.32e-2894
nervous system9.32e-2894
regional part of brain1.18e-2659
brain7.74e-2669
future brain7.74e-2669
regional part of forebrain1.70e-2541
forebrain1.70e-2541
future forebrain1.70e-2541
anterior neural tube2.53e-2442
telencephalon8.61e-2434
gray matter1.24e-2334
brain grey matter1.24e-2334
regional part of telencephalon4.87e-2333
pre-chordal neural plate1.82e-2261
cerebral hemisphere3.25e-2232
ectoderm-derived structure2.69e-21169
anterior region of body7.80e-21129
craniocervical region7.80e-21129
head3.03e-20123
ectoderm1.07e-19173
presumptive ectoderm1.07e-19173
tube1.41e-17194
cerebral cortex2.47e-1725
pallium2.47e-1725
embryo8.20e-17612
regional part of cerebral cortex1.39e-1622
cell layer1.59e-16312
epithelium1.87e-16309
multi-cellular organism9.82e-16659
organ part1.87e-15219
neocortex2.82e-1520
embryonic structure1.58e-14605
developing anatomical structure1.58e-14605
anatomical cluster3.11e-14286
multi-tissue structure3.74e-14347
germ layer3.95e-14604
embryonic tissue3.95e-14604
presumptive structure3.95e-14604
epiblast (generic)3.95e-14604
anatomical conduit5.10e-14241
organism subdivision7.58e-14365
anatomical system1.34e-13625
anatomical group2.09e-13626
posterior neural tube1.41e-0915
chordal neural plate1.41e-0915
organ2.99e-09511
segmental subdivision of nervous system2.45e-0813
nucleus of brain9.28e-089
neural nucleus9.28e-089
segmental subdivision of hindbrain1.03e-0712
hindbrain1.03e-0712
presumptive hindbrain1.03e-0712
basal ganglion1.57e-079
nuclear complex of neuraxis1.57e-079
aggregate regional part of brain1.57e-079
collection of basal ganglia1.57e-079
cerebral subcortex1.57e-079


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.