Personal tools

Coexpression cluster:C369

From FANTOM5_SSTAR

Revision as of 14:39, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C369_Lens_eye_Ciliary_retina_H9_Retinal_Renal



Phase1 CAGE Peaks

Hg19::chr11:31671561..31671580,+p@chr11:31671561..31671580
+
Hg19::chr13:104778247..104778293,+p@chr13:104778247..104778293
+
Hg19::chr13:36052713..36052724,-p@chr13:36052713..36052724
-
Hg19::chr15:79501729..79501736,+p1@MIR184
Hg19::chr15:95888661..95888665,+p@chr15:95888661..95888665
+
Hg19::chr19:40920692..40920700,-p@chr19:40920692..40920700
-
Hg19::chr19:51891222..51891233,-p1@LIM2
Hg19::chr1:147374915..147374932,+p1@GJA8
Hg19::chr20:35861148..35861151,+p@chr20:35861148..35861151
+
Hg19::chr22:25595823..25595826,+p1@CRYBB3
Hg19::chr22:25615541..25615544,+p2@CRYBB2
Hg19::chr2:45162900..45162914,-p1@ENST00000432125
Hg19::chr2:45162929..45162943,-p2@ENST00000432125
Hg19::chr2:45166428..45166437,-p4@ENST00000437916
Hg19::chr2:63196015..63196016,+p@chr2:63196015..63196016
+
Hg19::chr2:66670833..66670853,+p@chr2:66670833..66670853
+
Hg19::chr3:150690508..150690520,-p1@CLRN1
Hg19::chr3:150690540..150690556,-p2@CLRN1
Hg19::chr3:150690809..150690822,-p3@CLRN1
Hg19::chr3:62358596..62358618,-p3@FEZF2
Hg19::chr3:62358748..62358751,-p7@FEZF2
Hg19::chr3:98705008..98705016,-p@chr3:98705008..98705016
-
Hg19::chr3:98705040..98705081,-p@chr3:98705040..98705081
-
Hg19::chr4:8873531..8873542,-p4@HMX1
Hg19::chr4:8873545..8873583,-p1@HMX1
Hg19::chr6:80543084..80543091,-p@chr6:80543084..80543091
-
Hg19::chr8:123875589..123875604,+p24@ZHX2
Hg19::chr8:123875629..123875640,+p21@ZHX2
Hg19::chr8:36807609..36807626,-p@chr8:36807609..36807626
-
Hg19::chr9:75848662..75848671,-p@chr9:75848662..75848671
-


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:0005212structural constituent of eye lens1.27415068449798e-06
GO:0007601visual perception4.62678414592927e-06
GO:0050953sensory perception of light stimulus4.62678414592927e-06
GO:0007600sensory perception0.0010352899857421
GO:0032501multicellular organismal process0.0010352899857421
GO:0050877neurological system process0.0022444358804151
GO:0003008system process0.00405747896702666
GO:0050957equilibrioception0.0263556467090979
GO:0007043intercellular junction assembly0.0364949867660109
GO:0045494photoreceptor cell maintenance0.0364949867660109
GO:0050885neuromuscular process controlling balance0.0364949867660109
GO:0045216intercellular junction assembly and maintenance0.0364949867660109
GO:0030054cell junction0.0364949867660109
GO:0050905neuromuscular process0.0420995890852978
GO:0007028cytoplasm organization and biogenesis0.0420995890852978
GO:0005922connexon complex0.0448624819908534
GO:0006402mRNA catabolic process0.0448624819908534
GO:0005921gap junction0.0470365975887916
GO:0043010camera-type eye development0.0470365975887916



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>


Uber Anatomy
Ontology termp-valuen
regional part of nervous system7.32e-2494
nervous system7.32e-2494
central nervous system2.98e-2082
neural plate2.05e-1986
presumptive neural plate2.05e-1986
neurectoderm4.59e-1990
head1.70e-17123
anterior region of body2.07e-17129
craniocervical region2.07e-17129
brain6.31e-1769
future brain6.31e-1769
pre-chordal neural plate8.00e-1761
neural tube2.68e-1557
neural rod2.68e-1557
future spinal cord2.68e-1557
neural keel2.68e-1557
ectoderm-derived structure5.08e-15169
ectoderm5.11e-15173
presumptive ectoderm5.11e-15173
regional part of brain2.09e-1459
regional part of forebrain1.92e-1241
forebrain1.92e-1241
future forebrain1.92e-1241
anterior neural tube9.65e-1242
gray matter3.11e-1134
brain grey matter3.11e-1134
telencephalon4.04e-1134
cerebral hemisphere9.05e-1132
regional part of telencephalon1.04e-1033
embryo1.72e-10612
pigment epithelium of eye1.61e-0911
organism subdivision3.16e-09365
multi-tissue structure5.03e-09347
cerebral cortex1.71e-0825
pallium1.71e-0825
multi-cellular organism2.02e-08659
embryonic structure2.20e-08605
developing anatomical structure2.20e-08605
germ layer3.19e-08604
embryonic tissue3.19e-08604
presumptive structure3.19e-08604
epiblast (generic)3.19e-08604
anatomical system3.40e-08625
epithelium4.53e-08309
anatomical group4.93e-08626
cell layer6.25e-08312
anatomical conduit3.17e-07241
anatomical cluster4.68e-07286
eye5.65e-0720
regional part of cerebral cortex7.40e-0722
Disease
Ontology termp-valuen
ovarian cancer8.39e-0714


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.