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Coexpression cluster:C2081: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!4.69e-25!115;UBERON:0000062!1.31e-24!511;UBERON:0001049!1.10e-22!57;UBERON:0005068!1.10e-22!57;UBERON:0006241!1.10e-22!57;UBERON:0007135!1.10e-22!57;UBERON:0002616!2.17e-21!59;UBERON:0005743!2.16e-20!86;UBERON:0000955!2.51e-20!69;UBERON:0006238!2.51e-20!69;UBERON:0001017!7.53e-20!82;UBERON:0000073!1.38e-19!94;UBERON:0001016!1.38e-19!94;UBERON:0003075!9.88e-18!86;UBERON:0007284!9.88e-18!86;UBERON:0003080!1.99e-17!42;UBERON:0002780!2.55e-17!41;UBERON:0001890!2.55e-17!41;UBERON:0006240!2.55e-17!41;UBERON:0000480!2.44e-16!626;UBERON:0000468!3.63e-16!659;UBERON:0000467!3.73e-16!625;UBERON:0001893!1.32e-15!34;UBERON:0002020!1.34e-15!34;UBERON:0003528!1.34e-15!34;UBERON:0002346!2.14e-15!90;UBERON:0002791!5.48e-15!33;UBERON:0001869!2.68e-14!32;UBERON:0001474!2.71e-13!86;UBERON:0002371!4.76e-13!80;UBERON:0004765!3.32e-12!101;UBERON:0001434!3.32e-12!101;UBERON:0002050!3.55e-12!605;UBERON:0005423!3.55e-12!605;UBERON:0000923!4.88e-12!604;UBERON:0005291!4.88e-12!604;UBERON:0006598!4.88e-12!604;UBERON:0002532!4.88e-12!604;UBERON:0003056!4.95e-12!61;UBERON:0000922!2.57e-11!612;UBERON:0000033!5.52e-11!123;UBERON:0002619!6.92e-11!22;UBERON:0000956!1.94e-10!25;UBERON:0000203!1.94e-10!25;UBERON:0000153!5.90e-10!129;UBERON:0007811!5.90e-10!129;UBERON:0001950!9.08e-10!20;UBERON:0004121!2.39e-09!169;UBERON:0002390!6.93e-09!102;UBERON:0003061!6.93e-09!102;UBERON:0002405!1.33e-08!115;UBERON:0000924!2.70e-08!173;UBERON:0006601!2.70e-08!173;UBERON:0002193!6.38e-08!112;UBERON:0002308!7.13e-07!9;UBERON:0000125!7.13e-07!9
|ontology_enrichment_uberon=UBERON:0007023!4.69e-25!115;UBERON:0000062!1.31e-24!511;UBERON:0001049!1.10e-22!57;UBERON:0005068!1.10e-22!57;UBERON:0006241!1.10e-22!57;UBERON:0007135!1.10e-22!57;UBERON:0002616!2.17e-21!59;UBERON:0005743!2.16e-20!86;UBERON:0000955!2.51e-20!69;UBERON:0006238!2.51e-20!69;UBERON:0001017!7.53e-20!82;UBERON:0000073!1.38e-19!94;UBERON:0001016!1.38e-19!94;UBERON:0003075!9.88e-18!86;UBERON:0007284!9.88e-18!86;UBERON:0003080!1.99e-17!42;UBERON:0002780!2.55e-17!41;UBERON:0001890!2.55e-17!41;UBERON:0006240!2.55e-17!41;UBERON:0000480!2.44e-16!626;UBERON:0000468!3.63e-16!659;UBERON:0000467!3.73e-16!625;UBERON:0001893!1.32e-15!34;UBERON:0002020!1.34e-15!34;UBERON:0003528!1.34e-15!34;UBERON:0002346!2.14e-15!90;UBERON:0002791!5.48e-15!33;UBERON:0001869!2.68e-14!32;UBERON:0001474!2.71e-13!86;UBERON:0002371!4.76e-13!80;UBERON:0004765!3.32e-12!101;UBERON:0001434!3.32e-12!101;UBERON:0002050!3.55e-12!605;UBERON:0005423!3.55e-12!605;UBERON:0000923!4.88e-12!604;UBERON:0005291!4.88e-12!604;UBERON:0006598!4.88e-12!604;UBERON:0002532!4.88e-12!604;UBERON:0003056!4.95e-12!61;UBERON:0000922!2.57e-11!612;UBERON:0000033!5.52e-11!123;UBERON:0002619!6.92e-11!22;UBERON:0000956!1.94e-10!25;UBERON:0000203!1.94e-10!25;UBERON:0000153!5.90e-10!129;UBERON:0007811!5.90e-10!129;UBERON:0001950!9.08e-10!20;UBERON:0004121!2.39e-09!169;UBERON:0002390!6.93e-09!102;UBERON:0003061!6.93e-09!102;UBERON:0002405!1.33e-08!115;UBERON:0000924!2.70e-08!173;UBERON:0006601!2.70e-08!173;UBERON:0002193!6.38e-08!112;UBERON:0002308!7.13e-07!9;UBERON:0000125!7.13e-07!9
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}}
}}

Revision as of 13:38, 5 September 2012


Full id: C2081_corpus_medulla_substantia_pons_optic_thalamus_globus



Phase1 CAGE Peaks

Hg19::chr10:96162180..96162235,+p3@TBC1D12
Hg19::chr10:96162242..96162283,+p2@TBC1D12
Hg19::chr10:96162285..96162309,+p1@TBC1D12
Hg19::chr10:96162321..96162343,+p4@TBC1D12


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>

Uber Anatomy
Ontology termp-valuen
adult organism4.69e-25115
organ1.31e-24511
neural tube1.10e-2257
neural rod1.10e-2257
future spinal cord1.10e-2257
neural keel1.10e-2257
regional part of brain2.17e-2159
brain2.51e-2069
future brain2.51e-2069
central nervous system7.53e-2082
regional part of nervous system1.38e-1994
nervous system1.38e-1994
neural plate9.88e-1886
presumptive neural plate9.88e-1886
anterior neural tube1.99e-1742
regional part of forebrain2.55e-1741
forebrain2.55e-1741
future forebrain2.55e-1741
anatomical group2.44e-16626
multi-cellular organism3.63e-16659
anatomical system3.73e-16625
telencephalon1.32e-1534
gray matter1.34e-1534
brain grey matter1.34e-1534
neurectoderm2.14e-1590
regional part of telencephalon5.48e-1533
cerebral hemisphere2.68e-1432
bone element2.71e-1386
bone marrow4.76e-1380
skeletal element3.32e-12101
skeletal system3.32e-12101
embryonic structure3.55e-12605
developing anatomical structure3.55e-12605
germ layer4.88e-12604
embryonic tissue4.88e-12604
presumptive structure4.88e-12604
epiblast (generic)4.88e-12604
pre-chordal neural plate4.95e-1261
embryo2.57e-11612
head5.52e-11123
regional part of cerebral cortex6.92e-1122
cerebral cortex1.94e-1025
pallium1.94e-1025
anterior region of body5.90e-10129
craniocervical region5.90e-10129
neocortex9.08e-1020
ectoderm-derived structure2.39e-09169
hematopoietic system6.93e-09102
blood island6.93e-09102
immune system1.33e-08115
ectoderm2.70e-08173
presumptive ectoderm2.70e-08173
hemolymphoid system6.38e-08112
nucleus of brain7.13e-079
neural nucleus7.13e-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

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

TF#promotersEnrichmentp-valueq-value
CCNT2#90546.336201576962630.0006203100587215640.00511120806491688
E2F1#186944.907389214879320.001724022357361790.0106227239516524
E2F4#1874412.66806031528443.88145892637771e-050.000725439672176023
E2F6#187645.017155731697390.00157802193473060.00994791047512096
EBF1#187948.9064668465690.00015887907472010.00199341322497508
EGR1#195844.988179094810140.001615011500076050.0101248686029439
GABPB1#255347.067683836182170.0004006876864423170.00389677076863294
GATA3#2625427.2365163572061.81561517799785e-066.74088281460779e-05
HEY1#2346244.040111043105710.00375304636917980.0185457492193409
MAFK#7975427.10073313782991.85228494563408e-066.84055118235778e-05
MAX#414946.452555509007120.0005767613195645490.0048437098306531
MYC#460945.22228187160940.001344309395272740.00885514531270195
NFKB1#479045.488063424193840.001102199566301980.0076639560922112
NRF1#4899412.21027944771094.49717228915276e-050.000791640277611369
PAX5#507946.669565531177830.0005052774169483260.00443004265855156
PBX3#5090421.91451268674414.33289161192893e-060.000135933573763366
SP1#666745.69838137814090.0009482606065333980.0068295558572334
SP2#6668426.15353049384462.13562021071447e-067.73645644074953e-05
STAT1#6772420.70658749719925.43610708103893e-060.000164945260731152
TAF1#687243.343046285745290.008005664898701650.0321133675048203
TBP#690843.706770687096390.005296377814784350.0243420349673589
TCF12#6938410.63446490218647.8163066689251e-050.00119854243458504
USF1#739146.361499277207960.0006105011399140830.00506958166108666
YY1#752844.911170749853860.00171871838055440.0106592178709454
ZBTB7A#5134147.35190930787590.000342223540015990.00345863018151054
ZNF143#7702413.50087655222793.00867915035614e-050.000619403591137482
ZNF263#1012736.166381227758010.006539814347975980.0279567627476675



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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