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Coexpression cluster:C1012: Difference between revisions

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|full_id=C1012_heart_left_bile_Mast_epitheloid_aorta_umbilical
|full_id=C1012_heart_left_bile_Mast_epitheloid_aorta_umbilical
|id=C1012
|id=C1012
|ontology_enrichment_celltype=CL:0000183!6.65e-07!59;CL:0000393!7.06e-07!60;CL:0000211!7.06e-07!60
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.80e-31!115;UBERON:0000477!7.52e-22!286;UBERON:0000025!5.17e-20!194;UBERON:0000468!4.10e-19!659;UBERON:0001009!3.39e-16!113;UBERON:0004872!9.86e-16!84;UBERON:0004111!1.56e-15!241;UBERON:0000922!6.63e-15!612;UBERON:0004535!1.17e-14!110;UBERON:0000481!1.46e-14!347;UBERON:0000467!2.68e-13!625;UBERON:0002050!2.96e-13!605;UBERON:0005423!2.96e-13!605;UBERON:0000480!4.74e-13!626;UBERON:0000923!7.08e-13!604;UBERON:0005291!7.08e-13!604;UBERON:0006598!7.08e-13!604;UBERON:0002532!7.08e-13!604;UBERON:0000119!7.94e-13!312;UBERON:0000483!3.22e-12!309;UBERON:0001049!5.95e-12!57;UBERON:0005068!5.95e-12!57;UBERON:0006241!5.95e-12!57;UBERON:0007135!5.95e-12!57;UBERON:0002616!6.23e-12!59;UBERON:0002049!1.83e-11!79;UBERON:0007798!1.83e-11!79;UBERON:0001017!3.31e-11!82;UBERON:0003914!7.67e-11!118;UBERON:0005743!1.01e-10!86;UBERON:0001981!1.22e-10!60;UBERON:0007500!1.22e-10!60;UBERON:0004537!1.22e-10!60;UBERON:0006965!1.22e-10!60;UBERON:0000073!8.58e-10!94;UBERON:0001016!8.58e-10!94;UBERON:0000055!9.89e-10!69;UBERON:0007100!1.77e-09!27;UBERON:0003075!2.06e-09!86;UBERON:0007284!2.06e-09!86;UBERON:0002346!2.91e-09!90;UBERON:0000955!8.62e-09!69;UBERON:0006238!8.62e-09!69;UBERON:0002385!3.43e-08!63;UBERON:0001015!3.43e-08!63;UBERON:0000383!3.43e-08!63;UBERON:0001637!6.88e-08!42;UBERON:0003509!6.88e-08!42;UBERON:0004572!6.88e-08!42;UBERON:0003080!8.36e-08!42;UBERON:0000948!1.23e-07!24;UBERON:0005498!1.23e-07!24;UBERON:0004140!1.23e-07!24;UBERON:0009881!1.23e-07!24;UBERON:0004141!1.23e-07!24;UBERON:0003084!1.23e-07!24;UBERON:0007005!1.23e-07!24;UBERON:0004139!1.23e-07!24;UBERON:0004291!1.23e-07!24;UBERON:0002780!1.37e-07!41;UBERON:0001890!1.37e-07!41;UBERON:0006240!1.37e-07!41;UBERON:0001134!1.76e-07!61;UBERON:0002036!1.76e-07!61;UBERON:0003082!1.76e-07!61;UBERON:0000064!2.57e-07!219;UBERON:0001737!2.58e-07!9;UBERON:0003103!3.93e-07!69;UBERON:0000479!4.25e-07!787;UBERON:0002020!8.40e-07!34;UBERON:0003528!8.40e-07!34
|ontology_enrichment_uberon=UBERON:0007023!5.27e-31!114;UBERON:0000477!1.31e-15!373;UBERON:0011216!4.98e-14!223;UBERON:0000481!7.22e-13!342;UBERON:0000468!9.94e-12!656;UBERON:0001017!4.69e-11!81;UBERON:0001049!5.25e-11!56;UBERON:0005068!5.25e-11!56;UBERON:0006241!5.25e-11!56;UBERON:0007135!5.25e-11!56;UBERON:0001016!5.03e-10!89;UBERON:0000025!6.82e-10!192;UBERON:0000073!8.65e-10!53;UBERON:0002616!8.65e-10!53;UBERON:0002346!1.27e-09!86;UBERON:0003075!1.86e-09!82;UBERON:0007284!1.86e-09!82;UBERON:0000922!2.00e-09!592;UBERON:0000923!3.38e-09!560;UBERON:0010316!3.38e-09!560;UBERON:0005291!3.38e-09!560;UBERON:0006598!3.38e-09!560;UBERON:0010317!3.38e-09!560;UBERON:0002532!3.38e-09!560;UBERON:0002050!3.66e-09!564;UBERON:0001737!4.06e-09!9;UBERON:0004111!5.99e-09!240;UBERON:0005423!1.76e-08!581;UBERON:0010314!2.75e-08!132;UBERON:0000955!5.43e-08!68;UBERON:0006238!5.43e-08!68;UBERON:0000467!1.18e-07!624;UBERON:0000480!1.52e-07!625;UBERON:0004121!5.97e-07!171;UBERON:0000924!5.97e-07!171;UBERON:0006601!5.97e-07!171;UBERON:0001557!6.68e-07!19;UBERON:0002780!7.58e-07!41;UBERON:0001890!7.58e-07!41;UBERON:0003080!7.58e-07!41;UBERON:0006240!7.58e-07!41
|tf_chipseq_enrich=CTCF#10664;7:4.69022432644065:5.26249365325459e-05:0.000893528815887265!E2F1#1869;7:4.29396556301941:9.58670853279727e-05:0.00137004139635579!NANOG#79923;7:25.5891811708861:4.22843204062973e-10:4.1388304957013e-08!POLR2A#5430;8:2.14745317655807:0.00221072578897191:0.0127146864185493!TAF1#6872;6:2.50728471430897:0.0111173447561386:0.040881812928642!TBP#6908;7:3.24342435120934:0.000635422362049205:0.00521188063064925!ZNF263#10127;7:7.19411143238434:2.81251959700937e-06:9.7167295465452e-05
|tf_chipseq_enrich=CTCF#10664;7:4.69022432644065:5.26249365325459e-05:0.000893528815887265!E2F1#1869;7:4.29396556301941:9.58670853279727e-05:0.00137004139635579!NANOG#79923;7:25.5891811708861:4.22843204062973e-10:4.1388304957013e-08!POLR2A#5430;8:2.14745317655807:0.00221072578897191:0.0127146864185493!TAF1#6872;6:2.50728471430897:0.0111173447561386:0.040881812928642!TBP#6908;7:3.24342435120934:0.000635422362049205:0.00521188063064925!ZNF263#10127;7:7.19411143238434:2.81251959700937e-06:9.7167295465452e-05
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}}
}}

Revision as of 10:41, 19 October 2012


Full id: C1012_heart_left_bile_Mast_epitheloid_aorta_umbilical



Phase1 CAGE Peaks

Hg19::chr12:20521429..20521511,+p@chr12:20521429..20521511
+
Hg19::chr12:20522622..20522638,+p1@PDE3A
Hg19::chr12:20522763..20522783,+p5@PDE3A
Hg19::chr12:20522789..20522814,+p2@PDE3A
Hg19::chr12:20522816..20522841,+p4@PDE3A
Hg19::chr12:20522842..20522861,+p6@PDE3A
Hg19::chr12:20522891..20522907,+p8@PDE3A
Hg19::chr12:20523085..20523111,+p7@PDE3A


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism5.27e-31114
anatomical cluster1.31e-15373
organ system subdivision4.98e-14223
multi-tissue structure7.22e-13342
multi-cellular organism9.94e-12656
central nervous system4.69e-1181
neural tube5.25e-1156
neural rod5.25e-1156
future spinal cord5.25e-1156
neural keel5.25e-1156
nervous system5.03e-1089
tube6.82e-10192
regional part of nervous system8.65e-1053
regional part of brain8.65e-1053
neurectoderm1.27e-0986
neural plate1.86e-0982
presumptive neural plate1.86e-0982
embryo2.00e-09592
germ layer3.38e-09560
germ layer / neural crest3.38e-09560
embryonic tissue3.38e-09560
presumptive structure3.38e-09560
germ layer / neural crest derived structure3.38e-09560
epiblast (generic)3.38e-09560
embryonic structure3.66e-09564
larynx4.06e-099
anatomical conduit5.99e-09240
developing anatomical structure1.76e-08581
structure with developmental contribution from neural crest2.75e-08132
brain5.43e-0868
future brain5.43e-0868
anatomical system1.18e-07624
anatomical group1.52e-07625
ectoderm-derived structure5.97e-07171
ectoderm5.97e-07171
presumptive ectoderm5.97e-07171
upper respiratory tract6.68e-0719
regional part of forebrain7.58e-0741
forebrain7.58e-0741
anterior neural tube7.58e-0741
future forebrain7.58e-0741


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
CTCF#1066474.690224326440655.26249365325459e-050.000893528815887265
E2F1#186974.293965563019419.58670853279727e-050.00137004139635579
NANOG#79923725.58918117088614.22843204062973e-104.1388304957013e-08
POLR2A#543082.147453176558070.002210725788971910.0127146864185493
TAF1#687262.507284714308970.01111734475613860.040881812928642
TBP#690873.243424351209340.0006354223620492050.00521188063064925
ZNF263#1012777.194111432384342.81251959700937e-069.7167295465452e-05



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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