Personal tools

Coexpression cluster:C3396

From FANTOM5_SSTAR

Revision as of 16:18, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3396_brain_occipital_duodenum_temporal_parietal_small_Neurons



Phase1 CAGE Peaks

Hg19::chr14:103988483..103988543,-p3@CKB
Hg19::chr3:127347988..127348000,+p2@PODXL2
Hg19::chr3:127348005..127348063,+p1@PODXL2


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:0055064chloride ion homeostasis0.000883080183680678
GO:0055083monovalent inorganic anion homeostasis0.000883080183680678
GO:0030644cellular chloride ion homeostasis0.000883080183680678
GO:0030320cellular monovalent inorganic anion homeostasis0.000883080183680678
GO:0004111creatine kinase activity0.00282573181120752
GO:0055081anion homeostasis0.00302748067160046
GO:0030002cellular anion homeostasis0.00302748067160046
GO:0016775phosphotransferase activity, nitrogenous group as acceptor0.0141228361494071
GO:0005539glycosaminoglycan binding0.0407066168659049
GO:0030247polysaccharide binding0.0407066168659049
GO:0001871pattern binding0.0407066168659049
GO:0007420brain development0.0408329421154592



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
epithelial cell3.37e-07254
Uber Anatomy
Ontology termp-valuen
regional part of nervous system7.18e-3494
nervous system7.18e-3494
central nervous system2.85e-3282
neural tube1.41e-2857
neural rod1.41e-2857
future spinal cord1.41e-2857
neural keel1.41e-2857
neurectoderm1.41e-2790
brain2.40e-2669
future brain2.40e-2669
neural plate5.10e-2686
presumptive neural plate5.10e-2686
regional part of brain2.34e-2459
regional part of forebrain7.36e-2341
forebrain7.36e-2341
future forebrain7.36e-2341
anterior neural tube6.16e-2242
pre-chordal neural plate1.65e-2061
ectoderm2.65e-20173
presumptive ectoderm2.65e-20173
gray matter8.27e-2034
brain grey matter8.27e-2034
telencephalon1.18e-1934
regional part of telencephalon4.68e-1933
cerebral hemisphere5.43e-1932
ectoderm-derived structure5.59e-19169
adult organism3.39e-17115
head3.30e-16123
cerebral cortex2.92e-1525
pallium2.92e-1525
anterior region of body5.06e-15129
craniocervical region5.06e-15129
regional part of cerebral cortex2.70e-1422
organ part8.11e-14219
neocortex3.29e-1320
multi-tissue structure2.12e-11347
epithelium1.19e-10309
tube1.29e-10194
cell layer1.76e-10312
organ segment1.37e-0897
anatomical cluster2.15e-08286
organism subdivision6.15e-08365
anatomical conduit7.52e-08241
posterior neural tube8.62e-0815
chordal neural plate8.62e-0815
embryo3.70e-07612
segmental subdivision of nervous system6.22e-0713
Disease
Ontology termp-valuen
cell type cancer1.54e-15143
carcinoma7.70e-14106
cancer5.09e-10235
disease of cellular proliferation1.04e-09239


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
E2F1#186934.907389214879320.008460985347239390.0324277742634985
E2F6#187635.017155731697390.00791769806886330.0321182501597923
NFYA#4800212.28372046655370.008516011403724430.0324635440009335
NFYB#4801211.17319550235760.01025467135054530.0381134384761423
SETDB1#9869226.8800174520070.001814468907964410.0108915063094945
SP2#6668217.43568699589640.004273568481769740.0203097569470126



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.