Personal tools

Coexpression cluster:C1060: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 3: Line 3:
|gostat_on_coexpression_clusters=GO:0030128!clathrin coat of endocytic vesicle!0.022949948668774!160$GO:0030669!clathrin-coated endocytic vesicle membrane!0.022949948668774!160$GO:0030122!AP-2 adaptor complex!0.022949948668774!160$GO:0030666!endocytic vesicle membrane!0.022949948668774!160$GO:0004630!phospholipase D activity!0.022949948668774!23646$GO:0006895!Golgi to endosome transport!0.022949948668774!160$GO:0045334!clathrin-coated endocytic vesicle!0.022949948668774!160$GO:0030132!clathrin coat of coated pit!0.0372772031699452!160$GO:0030130!clathrin coat of trans-Golgi network vesicle!0.0376591196280217!160$GO:0012510!trans-Golgi network transport vesicle membrane!0.0376591196280217!160$GO:0006892!post-Golgi vesicle-mediated transport!0.0376591196280217!160$GO:0030125!clathrin vesicle coat!0.0376591196280217!160$GO:0030139!endocytic vesicle!0.0376591196280217!160$GO:0030665!clathrin coated vesicle membrane!0.0376591196280217!160$GO:0030140!trans-Golgi network transport vesicle!0.0431205011761095!160$GO:0030658!transport vesicle membrane!0.0431205011761095!160$GO:0030660!Golgi-associated vesicle membrane!0.0431205011761095!160
|gostat_on_coexpression_clusters=GO:0030128!clathrin coat of endocytic vesicle!0.022949948668774!160$GO:0030669!clathrin-coated endocytic vesicle membrane!0.022949948668774!160$GO:0030122!AP-2 adaptor complex!0.022949948668774!160$GO:0030666!endocytic vesicle membrane!0.022949948668774!160$GO:0004630!phospholipase D activity!0.022949948668774!23646$GO:0006895!Golgi to endosome transport!0.022949948668774!160$GO:0045334!clathrin-coated endocytic vesicle!0.022949948668774!160$GO:0030132!clathrin coat of coated pit!0.0372772031699452!160$GO:0030130!clathrin coat of trans-Golgi network vesicle!0.0376591196280217!160$GO:0012510!trans-Golgi network transport vesicle membrane!0.0376591196280217!160$GO:0006892!post-Golgi vesicle-mediated transport!0.0376591196280217!160$GO:0030125!clathrin vesicle coat!0.0376591196280217!160$GO:0030139!endocytic vesicle!0.0376591196280217!160$GO:0030665!clathrin coated vesicle membrane!0.0376591196280217!160$GO:0030140!trans-Golgi network transport vesicle!0.0431205011761095!160$GO:0030658!transport vesicle membrane!0.0431205011761095!160$GO:0030660!Golgi-associated vesicle membrane!0.0431205011761095!160
|id=C1060
|id=C1060
|ontology_enrichment_celltype=CL:0000055!4.19e-17!180;CL:0000222!2.45e-14!119;CL:0000183!5.42e-14!59;CL:0000187!7.29e-12!54;CL:0000680!7.41e-12!57;CL:0000056!7.41e-12!57;CL:0000355!7.41e-12!57;CL:0000393!2.62e-10!60;CL:0000211!2.62e-10!60;CL:0000192!2.75e-10!42;CL:0000514!2.75e-10!42;CL:0000220!2.14e-09!246;CL:0002321!5.29e-09!248;CL:0000359!5.02e-08!32
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000483!1.33e-28!309;UBERON:0000475!1.75e-28!365;UBERON:0000119!2.67e-28!312;UBERON:0000468!7.34e-24!659;UBERON:0004111!2.50e-23!241;UBERON:0000025!5.29e-23!194;UBERON:0000477!1.74e-22!286;UBERON:0000481!3.41e-22!347;UBERON:0000467!1.33e-19!625;UBERON:0000480!2.74e-19!626;UBERON:0002050!1.19e-17!605;UBERON:0005423!1.19e-17!605;UBERON:0000923!1.61e-17!604;UBERON:0005291!1.61e-17!604;UBERON:0006598!1.61e-17!604;UBERON:0002532!1.61e-17!604;UBERON:0000922!2.43e-17!612;UBERON:0003075!2.76e-17!86;UBERON:0007284!2.76e-17!86;UBERON:0002346!3.05e-16!90;UBERON:0000033!3.96e-16!123;UBERON:0002616!4.49e-16!59;UBERON:0004121!7.47e-16!169;UBERON:0001049!1.00e-15!57;UBERON:0005068!1.00e-15!57;UBERON:0006241!1.00e-15!57;UBERON:0007135!1.00e-15!57;UBERON:0000955!1.57e-15!69;UBERON:0006238!1.57e-15!69;UBERON:0000924!2.73e-15!173;UBERON:0006601!2.73e-15!173;UBERON:0007023!8.98e-15!115;UBERON:0005743!1.79e-14!86;UBERON:0000153!2.83e-14!129;UBERON:0007811!2.83e-14!129;UBERON:0003056!2.95e-14!61;UBERON:0000064!3.32e-14!219;UBERON:0001017!4.29e-14!82;UBERON:0000914!4.81e-14!83;UBERON:0002329!4.81e-14!83;UBERON:0003077!4.81e-14!83;UBERON:0003059!4.81e-14!83;UBERON:0007282!4.81e-14!83;UBERON:0009618!4.81e-14!83;UBERON:0007285!4.81e-14!83;UBERON:0000486!9.53e-14!82;UBERON:0005256!1.39e-13!143;UBERON:0004290!1.89e-13!70;UBERON:0002049!3.66e-13!79;UBERON:0007798!3.66e-13!79;UBERON:0000073!3.82e-13!94;UBERON:0001016!3.82e-13!94;UBERON:0004872!4.67e-13!84;UBERON:0001134!8.23e-13!61;UBERON:0002036!8.23e-13!61;UBERON:0003082!8.23e-13!61;UBERON:0001009!8.71e-13!113;UBERON:0002385!1.41e-12!63;UBERON:0001015!1.41e-12!63;UBERON:0000383!1.41e-12!63;UBERON:0003080!1.43e-12!42;UBERON:0002780!1.51e-12!41;UBERON:0001890!1.51e-12!41;UBERON:0006240!1.51e-12!41;UBERON:0001893!3.40e-12!34;UBERON:0003914!4.93e-12!118;UBERON:0001869!5.06e-12!32;UBERON:0004535!5.13e-12!110;UBERON:0002020!9.69e-12!34;UBERON:0003528!9.69e-12!34;UBERON:0002791!1.20e-11!33;UBERON:0000055!5.16e-11!69;UBERON:0002100!5.19e-11!216;UBERON:0002619!1.24e-10!22;UBERON:0001981!1.57e-10!60;UBERON:0007500!1.57e-10!60;UBERON:0004537!1.57e-10!60;UBERON:0006965!1.57e-10!60;UBERON:0000956!8.37e-10!25;UBERON:0000203!8.37e-10!25;UBERON:0001950!9.86e-10!20;UBERON:0000490!2.59e-09!138;UBERON:0001637!1.95e-08!42;UBERON:0003509!1.95e-08!42;UBERON:0004572!1.95e-08!42;UBERON:0003103!1.07e-07!69;UBERON:0004573!8.13e-07!33;UBERON:0004571!8.13e-07!33;UBERON:0000062!9.16e-07!511
}}
}}

Revision as of 14:06, 21 May 2012


Full id: C1060_Mesenchymal_Pericytes_Fibroblast_occipital_Renal_temporal_Nucleus



Phase1 CAGE Peaks

Hg19::chr19:1885483..1885507,-p1@FAM108A1
Hg19::chr19:2015699..2015748,-p1@BTBD2
Hg19::chr19:40854559..40854625,+p2@PLD3
Hg19::chr19:50270219..50270319,+p1@AP2A1
Hg19::chr19:7580944..7581031,+p1@ZNF358
Hg19::chr1:201857992..201858055,+p1@SHISA4
Hg19::chr4:102268904..102268948,+p1@FLJ20021
Hg19::chrX:48455870..48455905,+p1@WDR13


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:0030128clathrin coat of endocytic vesicle0.022949948668774
GO:0030669clathrin-coated endocytic vesicle membrane0.022949948668774
GO:0030122AP-2 adaptor complex0.022949948668774
GO:0030666endocytic vesicle membrane0.022949948668774
GO:0004630phospholipase D activity0.022949948668774
GO:0006895Golgi to endosome transport0.022949948668774
GO:0045334clathrin-coated endocytic vesicle0.022949948668774
GO:0030132clathrin coat of coated pit0.0372772031699452
GO:0030130clathrin coat of trans-Golgi network vesicle0.0376591196280217
GO:0012510trans-Golgi network transport vesicle membrane0.0376591196280217
GO:0006892post-Golgi vesicle-mediated transport0.0376591196280217
GO:0030125clathrin vesicle coat0.0376591196280217
GO:0030139endocytic vesicle0.0376591196280217
GO:0030665clathrin coated vesicle membrane0.0376591196280217
GO:0030140trans-Golgi network transport vesicle0.0431205011761095
GO:0030658transport vesicle membrane0.0431205011761095
GO:0030660Golgi-associated vesicle membrane0.0431205011761095



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>


Uber Anatomy
Ontology termp-valuen
epithelium1.33e-28309
organism subdivision1.75e-28365
cell layer2.67e-28312
multi-cellular organism7.34e-24659
anatomical conduit2.50e-23241
tube5.29e-23194
anatomical cluster1.74e-22286
multi-tissue structure3.41e-22347
anatomical system1.33e-19625
anatomical group2.74e-19626
embryonic structure1.19e-17605
developing anatomical structure1.19e-17605
germ layer1.61e-17604
embryonic tissue1.61e-17604
presumptive structure1.61e-17604
epiblast (generic)1.61e-17604
embryo2.43e-17612
neural plate2.76e-1786
presumptive neural plate2.76e-1786
neurectoderm3.05e-1690
head3.96e-16123
regional part of brain4.49e-1659
ectoderm-derived structure7.47e-16169
neural tube1.00e-1557
neural rod1.00e-1557
future spinal cord1.00e-1557
neural keel1.00e-1557
brain1.57e-1569
future brain1.57e-1569
ectoderm2.73e-15173
presumptive ectoderm2.73e-15173
adult organism8.98e-15115
anterior region of body2.83e-14129
craniocervical region2.83e-14129
pre-chordal neural plate2.95e-1461
organ part3.32e-14219
central nervous system4.29e-1482
somite4.81e-1483
paraxial mesoderm4.81e-1483
presomitic mesoderm4.81e-1483
presumptive segmental plate4.81e-1483
trunk paraxial mesoderm4.81e-1483
presumptive paraxial mesoderm4.81e-1483
multilaminar epithelium9.53e-1482
trunk mesenchyme1.39e-13143
dermomyotome1.89e-1370
vasculature3.66e-1379
vascular system3.66e-1379
regional part of nervous system3.82e-1394
nervous system3.82e-1394
splanchnic layer of lateral plate mesoderm4.67e-1384
skeletal muscle tissue8.23e-1361
striated muscle tissue8.23e-1361
myotome8.23e-1361
circulatory system8.71e-13113
muscle tissue1.41e-1263
musculature1.41e-1263
musculature of body1.41e-1263
anterior neural tube1.43e-1242
regional part of forebrain1.51e-1241
forebrain1.51e-1241
future forebrain1.51e-1241
telencephalon3.40e-1234
epithelial tube4.93e-12118
cerebral hemisphere5.06e-1232
cardiovascular system5.13e-12110
gray matter9.69e-1234
brain grey matter9.69e-1234
regional part of telencephalon1.20e-1133
vessel5.16e-1169
trunk5.19e-11216
regional part of cerebral cortex1.24e-1022
blood vessel1.57e-1060
epithelial tube open at both ends1.57e-1060
blood vasculature1.57e-1060
vascular cord1.57e-1060
cerebral cortex8.37e-1025
pallium8.37e-1025
neocortex9.86e-1020
unilaminar epithelium2.59e-09138
artery1.95e-0842
arterial blood vessel1.95e-0842
arterial system1.95e-0842
compound organ1.07e-0769


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.