Personal tools

Coexpression cluster:C256

From FANTOM5_SSTAR

Revision as of 18:24, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C256_occipital_caudate_amygdala_medial_thalamus_hippocampus_medulla



Phase1 CAGE Peaks

Hg19::chr10:83635586..83635597,+p6@NRG3
Hg19::chr11:10529999..10530000,-p3@MIR4485
Hg19::chr12:48111295..48111297,-p@chr12:48111295..48111297
-
Hg19::chr12:53438340..53438344,+p@chr12:53438340..53438344
+
Hg19::chr13:110775905..110775918,+p1@LOC283485
Hg19::chr14:101313715..101313726,-p3@AK126659
Hg19::chr14:101314924..101314935,-p@chr14:101314924..101314935
-
Hg19::chr14:102551227..102551242,+p@chr14:102551227..102551242
+
Hg19::chr14:73570140..73570193,-p@chr14:73570140..73570193
-
Hg19::chr15:34260460..34260472,+p2@CHRM5
Hg19::chr15:34260686..34260710,+p1@CHRM5
Hg19::chr15:69019611..69019647,+p@chr15:69019611..69019647
+
Hg19::chr16:68750222..68750228,+p@chr16:68750222..68750228
+
Hg19::chr17:22023159..22023161,+p@chr17:22023159..22023161
+
Hg19::chr18:32400519..32400523,-p@chr18:32400519..32400523
-
Hg19::chr19:45298867..45298869,+p@chr19:45298867..45298869
+
Hg19::chr1:204580692..204580695,-p@chr1:204580692..204580695
-
Hg19::chr1:24645071..24645074,+p@chr1:24645071..24645074
+
Hg19::chr22:49283073..49283079,+p@chr22:49283073..49283079
+
Hg19::chr2:165410518..165410520,+p@chr2:165410518..165410520
+
Hg19::chr2:220348295..220348300,+p@chr2:220348295..220348300
+
Hg19::chr2:70951535..70951538,+p@chr2:70951535..70951538
+
Hg19::chr3:14873451..14873452,+p@chr3:14873451..14873452
+
Hg19::chr3:88650202..88650205,+p1@ENST00000468361
Hg19::chr4:88415555..88415573,+p@chr4:88415555..88415573
+
Hg19::chr4:88447806..88447810,+p@chr4:88447806..88447810
+
Hg19::chr5:134259812..134259816,+p3@MTND6P4
Hg19::chr5:134260393..134260413,+p@chr5:134260393..134260413
+
Hg19::chr5:134263450..134263463,+p2@MIR4461
Hg19::chr5:134263476..134263487,+p6@MIR4461
Hg19::chr6:121756901..121756912,+p4@GJA1
Hg19::chr6:2911513..2911514,+p@chr6:2911513..2911514
+
Hg19::chr7:103179905..103179918,-p4@RELN
Hg19::chr7:105516839..105516841,+p10@CDHR3
Hg19::chr8:104184270..104184280,-p2@ENST00000521102
Hg19::chr8:131961464..131961485,+p@chr8:131961464..131961485
+
Hg19::chr8:24774826..24774901,-p@chr8:24774826..24774901
-
Hg19::chr8:24775032..24775050,-p@chr8:24775032..24775050
-
Hg19::chr8:24775054..24775104,-p@chr8:24775054..24775104
-
Hg19::chr8:24775187..24775201,-p@chr8:24775187..24775201
-
Hg19::chr8:24775491..24775536,-p@chr8:24775491..24775536
-
Hg19::chr8:24810309..24810339,+p2@CU691685
Hg19::chr9:2157655..2157669,+p24@SMARCA2
Hg19::chrM:1604..1614,+p1@uc004cor.1
Hg19::chrM:5322..5344,-p6@AK000561
Hg19::chrM:5715..5730,-p11@AK000561
Hg19::chrX:101380689..101380700,+p4@TCEAL2
Hg19::chrX:102632720..102632761,+p8@NGFRAP1
Hg19::chrX:138724994..138725023,-p2@MCF2
Hg19::chrX:20135072..20135077,-p9@MAP7D2
Hg19::chrX:46618069..46618072,+p@chrX:46618069..46618072
+


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:0032989cellular structure morphogenesis0.000399668203536365
GO:0000902cell morphogenesis0.000399668203536365
GO:0031175neurite development0.000399668203536365
GO:0048666neuron development0.000445259638768424
GO:0032990cell part morphogenesis0.000563980050971357
GO:0048858cell projection morphogenesis0.000563980050971357
GO:0030030cell projection organization and biogenesis0.000563980050971357
GO:0030182neuron differentiation0.000563980050971357
GO:0048699generation of neurons0.000765924806671898
GO:0022008neurogenesis0.000873649736739441
GO:0001764neuron migration0.00091837531401086
GO:0007242intracellular signaling cascade0.00091837531401086
GO:0032501multicellular organismal process0.00125855994145845
GO:0009653anatomical structure morphogenesis0.00143788039807146
GO:0007275multicellular organismal development0.00157067795046963
GO:0048468cell development0.00244710526549635
GO:0010232vascular transport0.00490369231408565
GO:0048731system development0.00533642506746418
GO:0048667neuron morphogenesis during differentiation0.00533642506746418
GO:0048812neurite morphogenesis0.00533642506746418
GO:0000904cellular morphogenesis during differentiation0.00533642506746418
GO:0032502developmental process0.00533642506746418
GO:0050794regulation of cellular process0.00533642506746418
GO:0016264gap junction assembly0.00533642506746418
GO:0015867ATP transport0.00533642506746418
GO:0051503adenine nucleotide transport0.00533642506746418
GO:0015865purine nucleotide transport0.00533642506746418
GO:0045844positive regulation of striated muscle development0.00533642506746418
GO:0007197muscarinic acetylcholine receptor, adenylate cyclase inhibiting pathway0.00533642506746418
GO:0048869cellular developmental process0.00533642506746418
GO:0030154cell differentiation0.00533642506746418
GO:0007399nervous system development0.00533642506746418
GO:0009966regulation of signal transduction0.0067577507656406
GO:0050789regulation of biological process0.0067577507656406
GO:0048856anatomical structure development0.0067577507656406
GO:0006862nucleotide transport0.0067577507656406
GO:0030297transmembrane receptor protein tyrosine kinase activator activity0.0067577507656406
GO:0015872dopamine transport0.00793685771538271
GO:0005771multivesicular body0.00793685771538271
GO:0043403skeletal muscle regeneration0.00793685771538271
GO:0002070epithelial cell maturation0.00793685771538271
GO:0030971receptor tyrosine kinase binding0.00793685771538271
GO:0065007biological regulation0.00850290002631808
GO:0048265response to pain0.00850290002631808
GO:0005916fascia adherens0.00850290002631808
GO:0002064epithelial cell development0.00850290002631808
GO:0005243gap junction channel activity0.00850290002631808
GO:0045732positive regulation of protein catabolic process0.00850290002631808
GO:0021511spinal cord patterning0.00850290002631808
GO:0016477cell migration0.00900988650186093
GO:0009790embryonic development0.00900988650186093
GO:0022829wide pore channel activity0.00943243420928138
GO:0030296protein tyrosine kinase activator activity0.00943243420928138
GO:0035050embryonic heart tube development0.010231206359391
GO:0007512adult heart development0.010231206359391
GO:0007213acetylcholine receptor signaling, muscarinic pathway0.010231206359391
GO:0009896positive regulation of catabolic process0.010231206359391
GO:0048513organ development0.0109249402049422
GO:0009268response to pH0.0109249402049422
GO:0051057positive regulation of small GTPase mediated signal transduction0.0109249402049422
GO:0004981muscarinic acetylcholine receptor activity0.0109249402049422
GO:0001947heart looping0.01209107719632
GO:0021510spinal cord development0.0132199216909085
GO:0033555multicellular organismal response to stress0.014913734021112
GO:0051924regulation of calcium ion transport0.014913734021112
GO:0016358dendrite development0.014913734021112
GO:0030295protein kinase activator activity0.014913734021112
GO:0005887integral to plasma membrane0.0150330141389711
GO:0007165signal transduction0.0150330141389711
GO:0031226intrinsic to plasma membrane0.0150330141389711
GO:0005913cell-cell adherens junction0.0150330141389711
GO:0016202regulation of striated muscle development0.0150330141389711
GO:0007243protein kinase cascade0.01554022287202
GO:0007043intercellular junction assembly0.01554022287202
GO:0030879mammary gland development0.01554022287202
GO:0006928cell motility0.0156024026347067
GO:0051674localization of cell0.0156024026347067
GO:0003007heart morphogenesis0.0168575278318891
GO:0042246tissue regeneration0.0168575278318891
GO:0043269regulation of ion transport0.0172516267171345
GO:0042176regulation of protein catabolic process0.0172516267171345
GO:0045216intercellular junction assembly and maintenance0.0172516267171345
GO:0007193G-protein signaling, adenylate cyclase inhibiting pathway0.0172516267171345
GO:0031099regeneration0.0172516267171345
GO:0019209kinase activator activity0.0172516267171345
GO:0030054cell junction0.0172516267171345
GO:0007154cell communication0.0172516267171345
GO:0016043cellular component organization and biogenesis0.0176900902268137
GO:0030165PDZ domain binding0.0184888344915059
GO:0017124SH3 domain binding0.0184888344915059
GO:0015464acetylcholine receptor activity0.0191979659125002
GO:0051056regulation of small GTPase mediated signal transduction0.0196776083318331
GO:0042166acetylcholine binding0.0196776083318331
GO:0007028cytoplasm organization and biogenesis0.021233740315628
GO:0009894regulation of catabolic process0.0218833993021424
GO:0005922connexon complex0.0242466077980364
GO:0010001glial cell differentiation0.0248511060954488
GO:0005921gap junction0.0288236293168925
GO:0042063gliogenesis0.029902594608196
GO:0030855epithelial cell differentiation0.029902594608196
GO:0048589developmental growth0.030425799462554
GO:0007267cell-cell signaling0.0319381431203324
GO:0018108peptidyl-tyrosine phosphorylation0.0335238577028587
GO:0008016regulation of heart contraction0.0335238577028587
GO:0018212peptidyl-tyrosine modification0.0342602000701058
GO:0043176amine binding0.0342602000701058
GO:0004434inositol or phosphatidylinositol phosphodiesterase activity0.0342602000701058
GO:0048469cell maturation0.0342602000701058
GO:0004435phosphoinositide phospholipase C activity0.0342602000701058
GO:0048732gland development0.0345091178567572
GO:0003015heart process0.0345091178567572
GO:0014704intercalated disc0.0345091178567572
GO:0060047heart contraction0.0345091178567572
GO:0005769early endosome0.0356546550359624
GO:0001701in utero embryonic development0.036062220017993
GO:0005770late endosome0.036462611212125
GO:0008283cell proliferation0.0372426018765522
GO:0021700developmental maturation0.0372426018765522
GO:0005912adherens junction0.037622550838198
GO:0007411axon guidance0.0385236784114739
GO:0044459plasma membrane part0.0385236784114739
GO:0004629phospholipase C activity0.0387241888721976
GO:0051259protein oligomerization0.0417571008387655
GO:0002009morphogenesis of an epithelium0.0420840877689062
GO:0008227amine receptor activity0.0443797674482315
GO:0006915apoptosis0.0450017594557596
GO:0012501programmed cell death0.0453442917401657
GO:0007264small GTPase mediated signal transduction0.0461864129273724
GO:0016265death0.0488876038405213
GO:0008219cell death0.0488876038405213
GO:0006836neurotransmitter transport0.0492438315404021



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><br>

Cell Type
Ontology termp-valuen
CD14-positive, CD16-negative classical monocyte3.38e-0742
classical monocyte8.89e-0745
Uber Anatomy
Ontology termp-valuen
neural tube3.05e-2957
neural rod3.05e-2957
future spinal cord3.05e-2957
neural keel3.05e-2957
central nervous system2.84e-2782
regional part of nervous system3.43e-2494
nervous system3.43e-2494
regional part of forebrain1.53e-2341
forebrain1.53e-2341
future forebrain1.53e-2341
anterior neural tube1.76e-2342
regional part of brain2.49e-2359
brain2.06e-2269
future brain2.06e-2269
neurectoderm1.27e-2190
neural plate1.67e-2086
presumptive neural plate1.67e-2086
gray matter1.16e-1934
brain grey matter1.16e-1934
telencephalon1.66e-1934
regional part of telencephalon6.46e-1933
cerebral hemisphere1.93e-1832
adult organism4.10e-18115
pre-chordal neural plate1.19e-1561
regional part of cerebral cortex3.80e-1522
cerebral cortex3.51e-1425
pallium3.51e-1425
neocortex7.09e-1420
ectoderm2.22e-11173
presumptive ectoderm2.22e-11173
ectoderm-derived structure1.52e-10169
head2.19e-10123
anterior region of body1.51e-09129
craniocervical region1.51e-09129
posterior neural tube5.13e-0715
chordal neural plate5.13e-0715
basal ganglion5.22e-079
nuclear complex of neuraxis5.22e-079
aggregate regional part of brain5.22e-079
collection of basal ganglia5.22e-079
cerebral subcortex5.22e-079
nucleus of brain5.43e-079
neural nucleus5.43e-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

"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C256&oldid=1990249"