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Coexpression cluster:C1108: Difference between revisions

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|full_id=C1108_Chondrocyte_Adipocyte_tenocyte_Preadipocyte_Osteoblast_mesenchymal_Myoblast
|full_id=C1108_Chondrocyte_Adipocyte_tenocyte_Preadipocyte_Osteoblast_mesenchymal_Myoblast
|id=C1108
|id=C1108
|ontology_enrichment_celltype=CL:0000055!2.94e-19!180;CL:0000057!1.03e-13!75;CL:0000136!5.66e-09!15;CL:0002334!2.58e-07!12;CL:0000680!3.05e-07!57;CL:0000056!3.05e-07!57;CL:0000355!3.05e-07!57
|ontology_enrichment_celltype=CL:0000057!5.10e-13!76;CL:0000136!3.94e-09!15;CL:0002334!1.40e-07!12;CL:0000680!1.71e-07!58;CL:0000056!1.71e-07!58;CL:0000355!1.71e-07!58;CL:0000183!4.57e-07!59;CL:0000055!5.24e-07!106
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!6.35e-26!365;UBERON:0000468!1.66e-22!659;UBERON:0000467!9.16e-19!625;UBERON:0000480!2.15e-18!626;UBERON:0000119!7.11e-15!312;UBERON:0000483!8.21e-15!309;UBERON:0000481!9.27e-15!347;UBERON:0000033!9.38e-14!123;UBERON:0002616!1.82e-13!59;UBERON:0004121!2.76e-13!169;UBERON:0000922!4.73e-13!612;UBERON:0002050!4.86e-13!605;UBERON:0005423!4.86e-13!605;UBERON:0000923!6.72e-13!604;UBERON:0005291!6.72e-13!604;UBERON:0006598!6.72e-13!604;UBERON:0002532!6.72e-13!604;UBERON:0000477!8.42e-13!286;UBERON:0001049!9.39e-13!57;UBERON:0005068!9.39e-13!57;UBERON:0006241!9.39e-13!57;UBERON:0007135!9.39e-13!57;UBERON:0000153!2.26e-12!129;UBERON:0007811!2.26e-12!129;UBERON:0001017!4.96e-12!82;UBERON:0005743!1.33e-11!86;UBERON:0000924!1.33e-11!173;UBERON:0006601!1.33e-11!173;UBERON:0000955!1.79e-11!69;UBERON:0006238!1.79e-11!69;UBERON:0004111!3.87e-11!241;UBERON:0000062!8.19e-11!511;UBERON:0000914!1.21e-10!83;UBERON:0002329!1.21e-10!83;UBERON:0003077!1.21e-10!83;UBERON:0003059!1.21e-10!83;UBERON:0007282!1.21e-10!83;UBERON:0009618!1.21e-10!83;UBERON:0007285!1.21e-10!83;UBERON:0003075!1.85e-10!86;UBERON:0007284!1.85e-10!86;UBERON:0003080!3.24e-10!42;UBERON:0002780!7.55e-10!41;UBERON:0001890!7.55e-10!41;UBERON:0006240!7.55e-10!41;UBERON:0000025!1.12e-09!194;UBERON:0000073!1.39e-09!94;UBERON:0001016!1.39e-09!94;UBERON:0003102!1.50e-09!95;UBERON:0007023!2.32e-09!115;UBERON:0000486!7.62e-09!82;UBERON:0005256!1.52e-08!143;UBERON:0000064!1.68e-08!219;UBERON:0002346!1.86e-08!90;UBERON:0003056!2.19e-08!61;UBERON:0002020!3.06e-08!34;UBERON:0003528!3.06e-08!34;UBERON:0001893!3.13e-08!34;UBERON:0004290!4.04e-08!70;UBERON:0002791!5.86e-08!33;UBERON:0002199!7.43e-08!45;UBERON:0002416!7.43e-08!45;UBERON:0001013!7.63e-08!14;UBERON:0002100!8.99e-08!216;UBERON:0001869!1.84e-07!32;UBERON:0000479!3.80e-07!787;UBERON:0001134!6.17e-07!61;UBERON:0002036!6.17e-07!61;UBERON:0003082!6.17e-07!61;UBERON:0002385!6.38e-07!63;UBERON:0001015!6.38e-07!63;UBERON:0000383!6.38e-07!63
|ontology_enrichment_uberon=UBERON:0000468!1.90e-19!656;UBERON:0000467!5.10e-17!624;UBERON:0000481!1.01e-16!342;UBERON:0000480!1.03e-16!625;UBERON:0000119!2.70e-14!309;UBERON:0000483!3.20e-14!306;UBERON:0010314!3.92e-14!132;UBERON:0010371!1.00e-13!104;UBERON:0001049!2.06e-13!56;UBERON:0005068!2.06e-13!56;UBERON:0006241!2.06e-13!56;UBERON:0007135!2.06e-13!56;UBERON:0000073!1.30e-12!53;UBERON:0002616!1.30e-12!53;UBERON:0004121!1.80e-12!171;UBERON:0000924!1.80e-12!171;UBERON:0006601!1.80e-12!171;UBERON:0001017!2.04e-12!81;UBERON:0000955!6.99e-12!68;UBERON:0006238!6.99e-12!68;UBERON:0003075!9.83e-12!82;UBERON:0007284!9.83e-12!82;UBERON:0000477!1.10e-11!373;UBERON:0002050!1.68e-11!564;UBERON:0005423!3.67e-11!581;UBERON:0000923!4.74e-11!560;UBERON:0010316!4.74e-11!560;UBERON:0005291!4.74e-11!560;UBERON:0006598!4.74e-11!560;UBERON:0010317!4.74e-11!560;UBERON:0002532!4.74e-11!560;UBERON:0002780!7.06e-11!41;UBERON:0001890!7.06e-11!41;UBERON:0003080!7.06e-11!41;UBERON:0006240!7.06e-11!41;UBERON:0000922!2.46e-10!592;UBERON:0004111!3.23e-10!240;UBERON:0001016!8.86e-10!89;UBERON:0002346!1.00e-09!86;UBERON:0007023!1.41e-09!114;UBERON:0001893!2.64e-09!34;UBERON:0003528!2.85e-09!34;UBERON:0002020!2.85e-09!34;UBERON:0007524!4.00e-09!73;UBERON:0000062!4.44e-09!503;UBERON:0000025!7.59e-09!192;UBERON:0003102!8.20e-09!99;UBERON:0003056!8.27e-09!61;UBERON:0003077!9.92e-09!72;UBERON:0007285!9.92e-09!72;UBERON:0000486!1.02e-08!83;UBERON:0002791!1.34e-08!32;UBERON:0000064!1.46e-08!218;UBERON:0001869!1.54e-08!32;UBERON:0007503!1.71e-08!78;UBERON:0002329!1.88e-08!71;UBERON:0003059!1.88e-08!71;UBERON:0007282!1.88e-08!71;UBERON:0004290!1.88e-08!71;UBERON:0009618!1.88e-08!71;UBERON:0001013!3.96e-08!14;UBERON:0000479!5.37e-08!773;UBERON:0011216!1.18e-07!223;UBERON:0002199!1.46e-07!46;UBERON:0002416!1.46e-07!46;UBERON:0003104!4.57e-07!160;UBERON:0009142!4.57e-07!160;UBERON:0002385!5.00e-07!64;UBERON:0001015!5.00e-07!64;UBERON:0000383!5.00e-07!64;UBERON:0001134!5.28e-07!62;UBERON:0002036!5.28e-07!62;UBERON:0003082!5.28e-07!62;UBERON:0000475!9.68e-07!264
|tf_chipseq_enrich=E2F1#1869;5:3.50527801062809:0.00509055358791505:0.0236826729996107
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}}
}}

Revision as of 10:51, 19 October 2012


Full id: C1108_Chondrocyte_Adipocyte_tenocyte_Preadipocyte_Osteoblast_mesenchymal_Myoblast



Phase1 CAGE Peaks

Hg19::chr10:124220985..124220996,+p5@HTRA1
Hg19::chr10:124221036..124221047,+p4@HTRA1
Hg19::chr10:124221061..124221080,+p2@HTRA1
Hg19::chr10:124221082..124221140,+p1@HTRA1
Hg19::chr10:124221146..124221166,+p3@HTRA1
Hg19::chr10:124248410..124248428,+p@chr10:124248410..124248428
+
Hg19::chr10:124248461..124248481,+p7@HTRA1


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
fibroblast5.10e-1376
fat cell3.94e-0915
preadipocyte1.40e-0712
muscle precursor cell1.71e-0758
myoblast1.71e-0758
multi-potent skeletal muscle stem cell1.71e-0758
contractile cell4.57e-0759
non-terminally differentiated cell5.24e-07106
Uber Anatomy
Ontology termp-valuen
multi-cellular organism1.90e-19656
anatomical system5.10e-17624
multi-tissue structure1.01e-16342
anatomical group1.03e-16625
cell layer2.70e-14309
epithelium3.20e-14306
structure with developmental contribution from neural crest3.92e-14132
ecto-epithelium1.00e-13104
neural tube2.06e-1356
neural rod2.06e-1356
future spinal cord2.06e-1356
neural keel2.06e-1356
regional part of nervous system1.30e-1253
regional part of brain1.30e-1253
ectoderm-derived structure1.80e-12171
ectoderm1.80e-12171
presumptive ectoderm1.80e-12171
central nervous system2.04e-1281
brain6.99e-1268
future brain6.99e-1268
neural plate9.83e-1282
presumptive neural plate9.83e-1282
anatomical cluster1.10e-11373
embryonic structure1.68e-11564
developing anatomical structure3.67e-11581
germ layer4.74e-11560
germ layer / neural crest4.74e-11560
embryonic tissue4.74e-11560
presumptive structure4.74e-11560
germ layer / neural crest derived structure4.74e-11560
epiblast (generic)4.74e-11560
regional part of forebrain7.06e-1141
forebrain7.06e-1141
anterior neural tube7.06e-1141
future forebrain7.06e-1141
embryo2.46e-10592
anatomical conduit3.23e-10240
nervous system8.86e-1089
neurectoderm1.00e-0986
adult organism1.41e-09114
telencephalon2.64e-0934
brain grey matter2.85e-0934
gray matter2.85e-0934
dense mesenchyme tissue4.00e-0973
organ4.44e-09503
tube7.59e-09192
surface structure8.20e-0999
pre-chordal neural plate8.27e-0961
paraxial mesoderm9.92e-0972
presumptive paraxial mesoderm9.92e-0972
multilaminar epithelium1.02e-0883
regional part of telencephalon1.34e-0832
organ part1.46e-08218
cerebral hemisphere1.54e-0832
epithelial vesicle1.71e-0878
somite1.88e-0871
presomitic mesoderm1.88e-0871
presumptive segmental plate1.88e-0871
dermomyotome1.88e-0871
trunk paraxial mesoderm1.88e-0871
adipose tissue3.96e-0814
tissue5.37e-08773
organ system subdivision1.18e-07223
integument1.46e-0746
integumental system1.46e-0746
mesenchyme4.57e-07160
entire embryonic mesenchyme4.57e-07160
muscle tissue5.00e-0764
musculature5.00e-0764
musculature of body5.00e-0764
skeletal muscle tissue5.28e-0762
striated muscle tissue5.28e-0762
myotome5.28e-0762
organism subdivision9.68e-07264


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
E2F1#186953.505278010628090.005090553587915050.0236826729996107



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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