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Coexpression cluster:C3517: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004121!5.22e-21!169;UBERON:0000924!1.23e-19!173;UBERON:0006601!1.23e-19!173;UBERON:0005743!1.04e-18!86;UBERON:0003075!2.71e-18!86;UBERON:0007284!2.71e-18!86;UBERON:0001017!2.38e-17!82;UBERON:0000481!3.28e-17!347;UBERON:0002346!2.13e-16!90;UBERON:0000073!2.46e-16!94;UBERON:0001016!2.46e-16!94;UBERON:0000064!3.50e-16!219;UBERON:0000119!1.75e-15!312;UBERON:0000483!2.35e-15!309;UBERON:0000153!4.51e-15!129;UBERON:0007811!4.51e-15!129;UBERON:0000033!6.69e-14!123;UBERON:0000475!1.02e-13!365;UBERON:0001049!2.23e-13!57;UBERON:0005068!2.23e-13!57;UBERON:0006241!2.23e-13!57;UBERON:0007135!2.23e-13!57;UBERON:0003056!2.96e-13!61;UBERON:0000955!8.65e-13!69;UBERON:0006238!8.65e-13!69;UBERON:0007023!3.61e-12!115;UBERON:0002616!1.10e-11!59;UBERON:0000025!3.22e-10!194;UBERON:0004111!1.26e-09!241;UBERON:0001008!1.96e-09!45;UBERON:0000489!3.61e-09!32;UBERON:0006554!3.99e-09!44;UBERON:0003080!4.57e-09!42;UBERON:0003103!4.90e-09!69;UBERON:0000922!6.33e-09!612;UBERON:0002780!9.33e-09!41;UBERON:0001890!9.33e-09!41;UBERON:0006240!9.33e-09!41;UBERON:0000477!9.80e-09!286;UBERON:0002020!3.22e-08!34;UBERON:0003528!3.22e-08!34;UBERON:0001869!4.11e-08!32;UBERON:0002113!6.80e-08!27;UBERON:0003918!6.80e-08!27;UBERON:0005095!6.80e-08!27;UBERON:0007687!6.80e-08!27;UBERON:0001893!9.79e-08!34;UBERON:0000956!1.11e-07!25;UBERON:0000203!1.11e-07!25;UBERON:0002791!1.53e-07!33;UBERON:0005177!3.27e-07!107;UBERON:0002050!4.54e-07!605;UBERON:0005423!4.54e-07!605;UBERON:0000923!7.87e-07!604;UBERON:0005291!7.87e-07!604;UBERON:0006598!7.87e-07!604;UBERON:0002532!7.87e-07!604
|ontology_enrichment_uberon=UBERON:0004121!5.22e-21!169;UBERON:0000924!1.23e-19!173;UBERON:0006601!1.23e-19!173;UBERON:0005743!1.04e-18!86;UBERON:0003075!2.71e-18!86;UBERON:0007284!2.71e-18!86;UBERON:0001017!2.38e-17!82;UBERON:0000481!3.28e-17!347;UBERON:0002346!2.13e-16!90;UBERON:0000073!2.46e-16!94;UBERON:0001016!2.46e-16!94;UBERON:0000064!3.50e-16!219;UBERON:0000119!1.75e-15!312;UBERON:0000483!2.35e-15!309;UBERON:0000153!4.51e-15!129;UBERON:0007811!4.51e-15!129;UBERON:0000033!6.69e-14!123;UBERON:0000475!1.02e-13!365;UBERON:0001049!2.23e-13!57;UBERON:0005068!2.23e-13!57;UBERON:0006241!2.23e-13!57;UBERON:0007135!2.23e-13!57;UBERON:0003056!2.96e-13!61;UBERON:0000955!8.65e-13!69;UBERON:0006238!8.65e-13!69;UBERON:0007023!3.61e-12!115;UBERON:0002616!1.10e-11!59;UBERON:0000025!3.22e-10!194;UBERON:0004111!1.26e-09!241;UBERON:0001008!1.96e-09!45;UBERON:0000489!3.61e-09!32;UBERON:0006554!3.99e-09!44;UBERON:0003080!4.57e-09!42;UBERON:0003103!4.90e-09!69;UBERON:0000922!6.33e-09!612;UBERON:0002780!9.33e-09!41;UBERON:0001890!9.33e-09!41;UBERON:0006240!9.33e-09!41;UBERON:0000477!9.80e-09!286;UBERON:0002020!3.22e-08!34;UBERON:0003528!3.22e-08!34;UBERON:0001869!4.11e-08!32;UBERON:0002113!6.80e-08!27;UBERON:0003918!6.80e-08!27;UBERON:0005095!6.80e-08!27;UBERON:0007687!6.80e-08!27;UBERON:0001893!9.79e-08!34;UBERON:0000956!1.11e-07!25;UBERON:0000203!1.11e-07!25;UBERON:0002791!1.53e-07!33;UBERON:0005177!3.27e-07!107;UBERON:0002050!4.54e-07!605;UBERON:0005423!4.54e-07!605;UBERON:0000923!7.87e-07!604;UBERON:0005291!7.87e-07!604;UBERON:0006598!7.87e-07!604;UBERON:0002532!7.87e-07!604
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}}
}}

Revision as of 12:59, 5 September 2012


Full id: C3517_Wilms_small_left_Dendritic_brain_adrenal_Placental



Phase1 CAGE Peaks

Hg19::chr15:78423705..78423738,-p2@CIB2
Hg19::chr15:78423763..78423774,-p3@CIB2
Hg19::chr15:78423776..78423794,-p1@CIB2


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

No GOStat results

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
ectodermal cell7.66e-0871
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure5.22e-21169
ectoderm1.23e-19173
presumptive ectoderm1.23e-19173
neural plate2.71e-1886
presumptive neural plate2.71e-1886
central nervous system2.38e-1782
multi-tissue structure3.28e-17347
neurectoderm2.13e-1690
regional part of nervous system2.46e-1694
nervous system2.46e-1694
organ part3.50e-16219
cell layer1.75e-15312
epithelium2.35e-15309
anterior region of body4.51e-15129
craniocervical region4.51e-15129
head6.69e-14123
organism subdivision1.02e-13365
neural tube2.23e-1357
neural rod2.23e-1357
future spinal cord2.23e-1357
neural keel2.23e-1357
pre-chordal neural plate2.96e-1361
brain8.65e-1369
future brain8.65e-1369
adult organism3.61e-12115
regional part of brain1.10e-1159
tube3.22e-10194
anatomical conduit1.26e-09241
renal system1.96e-0945
cavitated compound organ3.61e-0932
urinary system structure3.99e-0944
anterior neural tube4.57e-0942
compound organ4.90e-0969
embryo6.33e-09612
regional part of forebrain9.33e-0941
forebrain9.33e-0941
future forebrain9.33e-0941
anatomical cluster9.80e-09286
gray matter3.22e-0834
brain grey matter3.22e-0834
cerebral hemisphere4.11e-0832
kidney6.80e-0827
kidney mesenchyme6.80e-0827
kidney rudiment6.80e-0827
kidney field6.80e-0827
telencephalon9.79e-0834
cerebral cortex1.11e-0725
pallium1.11e-0725
regional part of telencephalon1.53e-0733
trunk region element3.27e-07107
embryonic structure4.54e-07605
developing anatomical structure4.54e-07605
germ layer7.87e-07604
embryonic tissue7.87e-07604
presumptive structure7.87e-07604
epiblast (generic)7.87e-07604


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

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

TF#promotersEnrichmentp-valueq-value
CCNT2#90536.336201576962630.003930750035764890.0189688385077742
CTCF#1066435.360256373075030.0064925092527670.0279018670829452
CTCFL#140690319.74647435897440.0001298372005551160.00171494465521384
E2F4#1874312.66806031528440.0004917987006298980.00436462988571431
E2F6#187635.017155731697390.00791769806886330.0321469684179145
EGR1#195834.988179094810140.008056488137383440.0319904024249179
ELF1#199734.258097958807540.01295179875054610.0461269534427377
ELK4#2005316.2356816584680.0002336043955745990.00255497009837842
ETS1#211339.728760922202340.001085840092584840.00761101029727971
GABPB1#255337.067683836182170.002832212825417420.0153882777688987
HMGN3#932438.178547723350590.001827766942164210.0108559003453531
PAX5#507936.669565531177830.003370290999677260.0172662524141712
RAD21#5885310.35503389545630.0009004912073565420.00663139199020659
SMC3#9126315.04493284493280.0002935825420371870.00308589644804969
YY1#752834.911170749853860.008441455341808260.0328691803162744
ZBTB7A#5134137.35190930787590.002516255860282270.013989632461646
ZEB1#6935316.88843201754390.0002075486917327580.00242435721014176
ZNF143#7702313.50087655222790.0004062804962997170.00388460393234881



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.

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