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Difference between revisions of "Coexpression cluster:C938"

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{{Coexpression_clusters
 
{{Coexpression_clusters
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|full_id=C938_leiomyoma_Smooth_Preadipocyte_hepatic_basal_Adipocyte_Ewing
 
|full_id=C938_leiomyoma_Smooth_Preadipocyte_hepatic_basal_Adipocyte_Ewing
 
|gostat_on_coexpression_clusters=GO:0016192!vesicle-mediated transport!0.00428373742142871!11015;378;90411$GO:0015031!protein transport!0.00428373742142871!11015;378;90411$GO:0045184!establishment of protein localization!0.00428373742142871!11015;378;90411$GO:0008104!protein localization!0.00428373742142871!11015;378;90411$GO:0033036!macromolecule localization!0.00428373742142871!11015;378;90411$GO:0005737!cytoplasm!0.00733327368124839!11015;92689;3069;378;90411$GO:0006810!transport!0.00972679873071346!11015;3069;378;90411$GO:0051234!establishment of localization!0.00972679873071346!11015;3069;378;90411$GO:0046923!ER retention sequence binding!0.00972679873071346!11015$GO:0006621!protein retention in ER!0.0104499899438909!11015$GO:0051179!localization!0.0104499899438909!11015;3069;378;90411$GO:0005048!signal sequence binding!0.0213109713755608!11015$GO:0032507!maintenance of cellular protein localization!0.0213109713755608!11015$GO:0051651!maintenance of cellular localization!0.0213109713755608!11015$GO:0045185!maintenance of protein localization!0.0213109713755608!11015$GO:0005794!Golgi apparatus!0.0213109713755608!378;90411$GO:0051235!maintenance of localization!0.0298119136755056!11015$GO:0005793!ER-Golgi intermediate compartment!0.0298119136755056!90411$GO:0005783!endoplasmic reticulum!0.0301261191994913!11015;90411$GO:0044424!intracellular part!0.0342977698170602!11015;92689;3069;378;90411$GO:0008203!cholesterol metabolic process!0.0462566618772057!3069
 
|gostat_on_coexpression_clusters=GO:0016192!vesicle-mediated transport!0.00428373742142871!11015;378;90411$GO:0015031!protein transport!0.00428373742142871!11015;378;90411$GO:0045184!establishment of protein localization!0.00428373742142871!11015;378;90411$GO:0008104!protein localization!0.00428373742142871!11015;378;90411$GO:0033036!macromolecule localization!0.00428373742142871!11015;378;90411$GO:0005737!cytoplasm!0.00733327368124839!11015;92689;3069;378;90411$GO:0006810!transport!0.00972679873071346!11015;3069;378;90411$GO:0051234!establishment of localization!0.00972679873071346!11015;3069;378;90411$GO:0046923!ER retention sequence binding!0.00972679873071346!11015$GO:0006621!protein retention in ER!0.0104499899438909!11015$GO:0051179!localization!0.0104499899438909!11015;3069;378;90411$GO:0005048!signal sequence binding!0.0213109713755608!11015$GO:0032507!maintenance of cellular protein localization!0.0213109713755608!11015$GO:0051651!maintenance of cellular localization!0.0213109713755608!11015$GO:0045185!maintenance of protein localization!0.0213109713755608!11015$GO:0005794!Golgi apparatus!0.0213109713755608!378;90411$GO:0051235!maintenance of localization!0.0298119136755056!11015$GO:0005793!ER-Golgi intermediate compartment!0.0298119136755056!90411$GO:0005783!endoplasmic reticulum!0.0301261191994913!11015;90411$GO:0044424!intracellular part!0.0342977698170602!11015;92689;3069;378;90411$GO:0008203!cholesterol metabolic process!0.0462566618772057!3069

Revision as of 09:44, 12 September 2012


Full id: C938_leiomyoma_Smooth_Preadipocyte_hepatic_basal_Adipocyte_Ewing



Phase1 CAGE Peaks

  Short description
Hg19::chr22:38864041..38864150,+ p1@KDELR3
Hg19::chr2:242212239..242212257,- p1@HDLBP
Hg19::chr2:47142884..47142955,- p1@MCFD2
Hg19::chr3:57583064..57583079,- p1@ARF4
Hg19::chr3:57583085..57583121,- p2@ARF4
Hg19::chr3:57583130..57583152,- p3@ARF4
Hg19::chr4:38869366..38869387,+ p3@FAM114A1
Hg19::chr4:38869393..38869404,+ p2@FAM114A1
Hg19::chr4:38869410..38869435,+ p1@FAM114A1


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0016192vesicle-mediated transport0.00428373742142871
GO:0015031protein transport0.00428373742142871
GO:0045184establishment of protein localization0.00428373742142871
GO:0008104protein localization0.00428373742142871
GO:0033036macromolecule localization0.00428373742142871
GO:0005737cytoplasm0.00733327368124839
GO:0006810transport0.00972679873071346
GO:0051234establishment of localization0.00972679873071346
GO:0046923ER retention sequence binding0.00972679873071346
GO:0006621protein retention in ER0.0104499899438909
GO:0051179localization0.0104499899438909
GO:0005048signal sequence binding0.0213109713755608
GO:0032507maintenance of cellular protein localization0.0213109713755608
GO:0051651maintenance of cellular localization0.0213109713755608
GO:0045185maintenance of protein localization0.0213109713755608
GO:0005794Golgi apparatus0.0213109713755608
GO:0051235maintenance of localization0.0298119136755056
GO:0005793ER-Golgi intermediate compartment0.0298119136755056
GO:0005783endoplasmic reticulum0.0301261191994913
GO:0044424intracellular part0.0342977698170602
GO:0008203cholesterol metabolic process0.0462566618772057



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Uber Anatomy
Ontology termp-valuen
trunk mesenchyme2.92e-26143
somite3.26e-2683
paraxial mesoderm3.26e-2683
presomitic mesoderm3.26e-2683
presumptive segmental plate3.26e-2683
trunk paraxial mesoderm3.26e-2683
presumptive paraxial mesoderm3.26e-2683
trunk2.25e-23216
dermomyotome3.61e-2370
multilaminar epithelium1.64e-2282
unilaminar epithelium1.06e-21138
vasculature3.77e-2179
vascular system3.77e-2179
skeletal muscle tissue7.60e-2161
striated muscle tissue7.60e-2161
myotome7.60e-2161
epithelial tube1.88e-20118
muscle tissue3.12e-2063
musculature3.12e-2063
musculature of body3.12e-2063
splanchnic layer of lateral plate mesoderm2.43e-1984
mesenchyme3.64e-19238
entire embryonic mesenchyme3.64e-19238
vessel4.66e-1869
blood vessel9.93e-1860
epithelial tube open at both ends9.93e-1860
blood vasculature9.93e-1860
vascular cord9.93e-1860
artery1.13e-1742
arterial blood vessel1.13e-1742
arterial system1.13e-1742
organism subdivision3.76e-17365
multi-cellular organism2.25e-15659
systemic artery1.17e-1433
systemic arterial system1.17e-1433
cardiovascular system3.68e-14110
multi-tissue structure6.38e-14347
mesoderm8.09e-14448
mesoderm-derived structure8.09e-14448
presumptive mesoderm8.09e-14448
circulatory system1.16e-13113
anatomical system2.18e-12625
anatomical group2.42e-12626
surface structure7.68e-1295
cell layer8.19e-12312
epithelium3.17e-11309
anatomical cluster6.36e-10286
integument1.18e-0845
integumental system1.18e-0845
embryonic structure5.77e-08605
developing anatomical structure5.77e-08605
anatomical conduit5.89e-08241
aorta7.53e-0821
aortic system7.53e-0821
germ layer7.59e-08604
embryonic tissue7.59e-08604
presumptive structure7.59e-08604
epiblast (generic)7.59e-08604
embryo1.28e-07612
skin of body1.82e-0740
Disease
Ontology termp-valuen
ovarian cancer1.25e-0714


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ATF3#46737.487724842002920.006050357420552810.0268411043515893
BATF#1053838.119267264101210.004821448895817150.0226242216484812
BRCA1#67236.728076881074590.008149333567200950.0321804389150371
CCNT2#90585.632179179522342.97597445628313e-060.000101075706094229
CHD2#110644.597343481829710.007379358397557620.0304971236469677
CTCFL#14069036.582158119658120.008659511962914930.032961249722825
E2F1#186984.36212374655942.18983367577486e-050.000481380844589036
E2F4#187445.630249029015310.003536571815964610.0179473286631452
E2F6#187673.902232235764630.0003067423599492730.00316341121069835
EGR1#195873.8796948515190.0003186557858542290.00326275408027744
ELK4#200547.215858514874680.001409539058987380.00916573375142164
ETS1#211377.566814050601823.61164439627206e-060.000118689908465153
GABPB1#255353.926491020101210.004337976092287310.0205868080657243
HEY1#2346294.040111043105713.4850025352467e-060.000116024921829337
HMGN3#932476.361092673717131.17234969197953e-050.000298122789093379
MAFF#23764318.77178549664840.0004336934263990230.00404921399603858
MAFK#797539.033577712609970.003567854712813750.0180841144553048
MEF2A#420536.247743636548020.01000005008462560.0374993799428462
NFYB#480135.586597751178820.01358500277111940.0479536318117056
NRF1#489945.426790865649290.004046698912068520.0193672984913172
POLR2A#543092.147453176558070.001029412892608020.00728936559028337
REST#597844.288901651612450.009457025945962830.0356692789010622
RFX5#599345.354627034308930.004249445027674740.0202217974778021
SIX5#14791235.6955717851530.01288794699034820.0463563953617915
SRF#672269.19811884144521.00386889165062e-050.000263094261418065
TAF1#687293.343046285745291.91655056102793e-050.000433627868377809
TFAP2C#702244.804101604382320.006299303434747120.0277885090357573
THAP1#55145310.45638153428380.002353923504026620.0133413695575534
ZBTB7A#5134154.084394059931050.003634990312833990.0183753510785126
ZEB1#693535.629477339181290.01330488236341950.047039560228611



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.