Personal tools

Coexpression cluster:C2798

From FANTOM5_SSTAR

Revision as of 15:34, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2798_seminal_ductus_hippocampus_putamen_parietal_amygdala_caudate



Phase1 CAGE Peaks

Hg19::chr4:95917409..95917421,+p11@BMPR1B
Hg19::chr5:131317011..131317016,-p@chr5:131317011..131317016
-
Hg19::chr5:131335358..131335378,-p3@ACSL6
Hg19::chr5:131335380..131335396,-p4@ACSL6


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:0001550ovarian cumulus expansion0.00532783868959813
GO:0048165fused antrum stage, oogenesis0.00532783868959813
GO:0001547antral ovarian follicle growth0.00532783868959813
GO:0022605oogenesis stage0.00532783868959813
GO:0000287magnesium ion binding0.00625347626226086
GO:0005025transforming growth factor beta receptor activity, type I0.0106550500303272
GO:0015645fatty-acid ligase activity0.0112798249239386
GO:0004467long-chain-fatty-acid-CoA ligase activity0.0112798249239386
GO:0001502cartilage condensation0.0112798249239386
GO:0046332SMAD binding0.0112798249239386
GO:0006637acyl-CoA metabolic process0.0112798249239386
GO:0048477oogenesis0.0112798249239386
GO:0007405neuroblast proliferation0.0112798249239386
GO:0030509BMP signaling pathway0.0112798249239386
GO:0004675transmembrane receptor protein serine/threonine kinase activity0.0112798249239386
GO:0005024transforming growth factor beta receptor activity0.0112798249239386
GO:0001541ovarian follicle development0.0112798249239386
GO:0022601menstrual cycle phase0.0118754373208547
GO:0022602menstrual cycle process0.0118754373208547
GO:0008585female gonad development0.0118754373208547
GO:0009953dorsal/ventral pattern formation0.0118754373208547
GO:0016877ligase activity, forming carbon-sulfur bonds0.0118754373208547
GO:0046545development of primary female sexual characteristics0.0118754373208547
GO:0046660female sex differentiation0.0118754373208547
GO:0042698menstrual cycle0.0118754373208547
GO:0043010camera-type eye development0.0118754373208547
GO:0007292female gamete generation0.0118754373208547
GO:0051216cartilage development0.0118754373208547
GO:0060173limb development0.0118754373208547
GO:0035107appendage morphogenesis0.0118754373208547
GO:0035108limb morphogenesis0.0118754373208547
GO:0048589developmental growth0.0118754373208547
GO:0048736appendage development0.0118754373208547
GO:0048731system development0.0118754373208547
GO:0031903microbody membrane0.0122269174325372
GO:0005778peroxisomal membrane0.0122269174325372
GO:0044439peroxisomal part0.0122269174325372
GO:0044438microbody part0.0122269174325372
GO:0045597positive regulation of cell differentiation0.0122269174325372
GO:0001654eye development0.0122269174325372
GO:0048869cellular developmental process0.0122269174325372
GO:0030154cell differentiation0.0122269174325372
GO:0008406gonad development0.0125838056125745
GO:0048608reproductive structure development0.0125838056125745
GO:0048856anatomical structure development0.0135298304788747
GO:0045137development of primary sexual characteristics0.0135298304788747
GO:0048609reproductive process in a multicellular organism0.0135298304788747
GO:0032504multicellular organism reproduction0.0135298304788747
GO:0051094positive regulation of developmental process0.0147731056398816
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0159343656977792
GO:0004702receptor signaling protein serine/threonine kinase activity0.0159343656977792
GO:0007275multicellular organismal development0.0159343656977792
GO:0007548sex differentiation0.0161617906101618
GO:0005741mitochondrial outer membrane0.0161617906101618
GO:0007423sensory organ development0.0162435810661104
GO:0003002regionalization0.0162435810661104
GO:0003006reproductive developmental process0.0162435810661104
GO:0031968organelle outer membrane0.0170629428085416
GO:0019867outer membrane0.0173140632093917
GO:0042579microbody0.0174431267736113
GO:0005777peroxisome0.0174431267736113
GO:0043235receptor complex0.0188751820253275
GO:0007389pattern specification process0.0209354184380529
GO:0019199transmembrane receptor protein kinase activity0.0211059568177126
GO:0045595regulation of cell differentiation0.0235570851566974
GO:0030145manganese ion binding0.0236824483250839
GO:0005792microsome0.0257037987277299
GO:0032502developmental process0.0258298488267971
GO:0042598vesicular fraction0.02603453710581
GO:0005057receptor signaling protein activity0.0268742409044643
GO:0006631fatty acid metabolic process0.0285855311650691
GO:0001501skeletal development0.0308368239405674
GO:0005886plasma membrane0.0309517442921071
GO:0032501multicellular organismal process0.0309517442921071
GO:0050793regulation of developmental process0.0334143824400436
GO:0048699generation of neurons0.0338100634234986
GO:0022008neurogenesis0.0359262911726028
GO:0007276gamete generation0.0359262911726028
GO:0032787monocarboxylic acid metabolic process0.0381186699285198
GO:0006732coenzyme metabolic process0.0381186699285198
GO:0006954inflammatory response0.0381186699285198
GO:0007167enzyme linked receptor protein signaling pathway0.0385177082049996
GO:0009888tissue development0.0385177082049996
GO:0022414reproductive process0.0385177082049996
GO:0019953sexual reproduction0.0393067648118722
GO:0051186cofactor metabolic process0.0422844170472928
GO:0016337cell-cell adhesion0.0422844170472928
GO:0031966mitochondrial membrane0.0491083704470924



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
neural tube2.12e-7057
neural rod2.12e-7057
future spinal cord2.12e-7057
neural keel2.12e-7057
adult organism1.11e-61115
central nervous system4.26e-5982
regional part of brain9.13e-5959
brain3.54e-5669
future brain3.54e-5669
regional part of forebrain2.37e-5341
forebrain2.37e-5341
future forebrain2.37e-5341
regional part of nervous system5.99e-5294
nervous system5.99e-5294
anterior neural tube8.96e-5242
neural plate1.91e-5186
presumptive neural plate1.91e-5186
neurectoderm2.72e-4890
gray matter1.03e-4634
brain grey matter1.03e-4634
telencephalon1.26e-4634
regional part of telencephalon4.20e-4533
cerebral hemisphere9.26e-4432
pre-chordal neural plate8.86e-3961
regional part of cerebral cortex1.95e-3522
cerebral cortex8.52e-3325
pallium8.52e-3325
neocortex3.75e-3220
anterior region of body4.83e-31129
craniocervical region4.83e-31129
head6.67e-30123
ectoderm-derived structure8.31e-25169
ectoderm9.02e-24173
presumptive ectoderm9.02e-24173
posterior neural tube7.21e-1915
chordal neural plate7.21e-1915
tube1.17e-17194
basal ganglion1.69e-159
nuclear complex of neuraxis1.69e-159
aggregate regional part of brain1.69e-159
collection of basal ganglia1.69e-159
cerebral subcortex1.69e-159
nucleus of brain2.89e-159
neural nucleus2.89e-159
segmental subdivision of hindbrain1.35e-1412
hindbrain1.35e-1412
presumptive hindbrain1.35e-1412
anatomical conduit6.18e-14241
segmental subdivision of nervous system3.09e-1313
temporal lobe3.51e-137
telencephalic nucleus2.80e-127
anatomical cluster2.60e-11286
epithelium1.15e-10309
cell layer2.26e-10312
gyrus2.32e-106
regional part of metencephalon2.46e-109
metencephalon2.46e-109
future metencephalon2.46e-109
brainstem4.53e-108
limbic system1.04e-095
organism subdivision3.21e-09365
parietal lobe3.79e-095
organ part1.49e-08219
occipital lobe1.62e-085
multi-tissue structure3.18e-08347
diencephalon4.23e-087
future diencephalon4.23e-087
corpus striatum4.30e-084
striatum4.30e-084
ventral part of telencephalon4.30e-084
future corpus striatum4.30e-084
organ6.74e-07511


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:C2798&oldid=2137515"