Personal tools

Coexpression cluster:C445

From FANTOM5_SSTAR

Revision as of 20:02, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C445_lung_Lens_Ciliary_diencephalon_thalamus_bile_hepatoma



Phase1 CAGE Peaks

Hg19::chr11:31014065..31014073,-p1@DCDC5
Hg19::chr15:52161504..52161511,+p@chr15:52161504..52161511
+
Hg19::chr15:99387143..99387153,-p@chr15:99387143..99387153
-
Hg19::chr1:114654778..114654823,+p@chr1:114654778..114654823
+
Hg19::chr20:388056..388067,+p10@RBCK1
Hg19::chr3:178968900..178968909,-p5@KCNMB3
Hg19::chr5:175298120..175298129,-p@chr5:175298120..175298129
-
Hg19::chr5:175298177..175298187,+p38@CPLX2
Hg19::chr7:107883547..107883552,-p30@NRCAM
Hg19::chr7:107883582..107883593,-p20@NRCAM
Hg19::chr7:107883608..107883632,-p15@NRCAM
Hg19::chr7:107883640..107883652,-p21@NRCAM
Hg19::chr7:107883678..107883689,-p13@NRCAM
Hg19::chr7:107883711..107883718,-p29@NRCAM
Hg19::chr7:107883761..107883772,-p18@NRCAM
Hg19::chr7:107883776..107883779,-p37@NRCAM
Hg19::chr7:107883785..107883799,-p12@NRCAM
Hg19::chr7:107883809..107883820,-p11@NRCAM
Hg19::chr7:107883821..107883841,-p7@NRCAM
Hg19::chr7:11676048..11676067,-p23@THSD7A
Hg19::chr7:134212246..134212265,+p3@AKR1B10
Hg19::chr7:134220360..134220368,+p@chr7:134220360..134220368
+


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:0045162clustering of voltage-gated sodium channels0.0269574158313691
GO:0045666positive regulation of neuron differentiation0.0269574158313691
GO:0019228generation of action potential0.0269574158313691
GO:0045161neuronal ion channel clustering0.0269574158313691
GO:0007413axonal fasciculation0.0269574158313691
GO:0030506ankyrin binding0.0269574158313691
GO:0043303mast cell degranulation0.0269574158313691
GO:0002448mast cell mediated immunity0.0269574158313691
GO:0045576mast cell activation0.0269574158313691
GO:0043299leukocyte degranulation0.0269574158313691
GO:0005513detection of calcium ion0.0269574158313691
GO:0002444myeloid leukocyte mediated immunity0.027790017114087
GO:0042551neuron maturation0.027790017114087
GO:0008038neuron recognition0.027790017114087
GO:0030516regulation of axon extension0.027790017114087
GO:0004033aldo-keto reductase activity0.027790017114087
GO:0048675axon extension0.0350845861841104
GO:0015459potassium channel regulator activity0.0350845861841104
GO:0009593detection of chemical stimulus0.0350845861841104
GO:0019905syntaxin binding0.0351789369391645
GO:0000149SNARE binding0.0370239210486011
GO:0006081aldehyde metabolic process0.0379096057419114
GO:0007416synaptogenesis0.0379096057419114
GO:0050770regulation of axonogenesis0.0379096057419114
GO:0045664regulation of neuron differentiation0.0379096057419114
GO:0002274myeloid leukocyte activation0.0379096057419114
GO:0042391regulation of membrane potential0.0379096057419114
GO:0015269calcium-activated potassium channel activity0.0379096057419114
GO:0022839ion gated channel activity0.0379096057419114
GO:0006904vesicle docking during exocytosis0.0379096057419114
GO:0005227calcium activated cation channel activity0.0379096057419114
GO:0016247channel regulator activity0.0379096057419114
GO:0001764neuron migration0.0379096057419114
GO:0048278vesicle docking0.0379096057419114
GO:0008037cell recognition0.0379096057419114
GO:0022406membrane docking0.0379096057419114
GO:0050767regulation of neurogenesis0.0379096057419114
GO:0050808synapse organization and biogenesis0.0379096057419114
GO:0001508regulation of action potential0.0379096057419114
GO:0048469cell maturation0.0415637487495041
GO:0045597positive regulation of cell differentiation0.0423447442564664
GO:0009897external side of plasma membrane0.0439633943978233
GO:0045055regulated secretory pathway0.0444711836814443
GO:0021700developmental maturation0.0444711836814443



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 cell7.13e-07254
Uber Anatomy
Ontology termp-valuen
neural plate5.51e-1786
presumptive neural plate5.51e-1786
neural tube4.51e-1657
neural rod4.51e-1657
future spinal cord4.51e-1657
neural keel4.51e-1657
adult organism4.73e-16115
neurectoderm5.20e-1690
regional part of forebrain1.85e-1541
forebrain1.85e-1541
future forebrain1.85e-1541
anterior neural tube9.37e-1542
regional part of brain1.72e-1459
brain2.33e-1469
future brain2.33e-1469
pre-chordal neural plate6.19e-1461
central nervous system2.42e-1382
telencephalon3.23e-1334
gray matter8.81e-1334
brain grey matter8.81e-1334
regional part of nervous system9.37e-1394
nervous system9.37e-1394
regional part of telencephalon1.33e-1233
cerebral hemisphere2.05e-1232
ectoderm-derived structure1.21e-10169
head1.99e-10123
ectoderm2.91e-10173
presumptive ectoderm2.91e-10173
anterior region of body3.09e-10129
craniocervical region3.09e-10129
organ4.23e-08511
neocortex7.97e-0820
cerebral cortex8.60e-0825
pallium8.60e-0825
regional part of cerebral cortex1.85e-0722
basal ganglion2.24e-079
nuclear complex of neuraxis2.24e-079
aggregate regional part of brain2.24e-079
collection of basal ganglia2.24e-079
cerebral subcortex2.24e-079
organ part3.40e-07219
nucleus of brain4.77e-079
neural nucleus4.77e-079
Disease
Ontology termp-valuen
carcinoma1.75e-12106
disease of cellular proliferation8.02e-10239
cell type cancer8.22e-10143
cancer1.29e-09235


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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C445&oldid=1993476"