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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.143931545137586,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.307583768619467,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.32832365318808,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.823456809183704,0.288523274754883,0.542256904750742,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0267975841371139,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|full_id=C308_lung_Hepatocyte_liver_thyroid_heart_left_breast
|full_id=C308_lung_Hepatocyte_liver_thyroid_heart_left_breast
|gostat_on_coexpression_clusters=GO:0001101!response to acid!0.0102944784231565!27159$GO:0010383!cell wall polysaccharide metabolic process!0.0102944784231565!27159$GO:0006037!cell wall chitin metabolic process!0.0102944784231565!27159$GO:0010037!response to carbon dioxide!0.0102944784231565!2$GO:0005615!extracellular space!0.0102944784231565!27159;6439;8547$GO:0045029!UDP-activated nucleotide receptor activity!0.0155385513714468!9934$GO:0019959!interleukin-8 binding!0.0155385513714468!2$GO:0015065!uridine nucleotide receptor activity!0.0155385513714468!9934$GO:0017114!wide-spectrum protease inhibitor activity!0.0155385513714468!2$GO:0050828!regulation of liquid surface tension!0.0209143579160127!6439$GO:0008061!chitin binding!0.0209143579160127!27159$GO:0044421!extracellular region part!0.0209143579160127!27159;6439;8547$GO:0043120!tumor necrosis factor binding!0.0279299039569851!2$GO:0019966!interleukin-1 binding!0.0279299039569851!2$GO:0051384!response to glucocorticoid stimulus!0.0279299039569851!2$GO:0019958!C-X-C chemokine binding!0.0279299039569851!2$GO:0003796!lysozyme activity!0.0279299039569851!27159$GO:0031960!response to corticosteroid stimulus!0.0279299039569851!2$GO:0005529!sugar binding!0.0279299039569851!27159;8547$GO:0006032!chitin catabolic process!0.0279299039569851!27159$GO:0006046!N-acetylglucosamine catabolic process!0.0279299039569851!27159$GO:0006043!glucosamine catabolic process!0.0279299039569851!27159$GO:0046348!amino sugar catabolic process!0.0279299039569851!27159$GO:0006030!chitin metabolic process!0.0279299039569851!27159$GO:0004568!chitinase activity!0.0279299039569851!27159$GO:0009620!response to fungus!0.0325618814526327!27159$GO:0010382!cell wall metabolic process!0.0325618814526327!27159$GO:0007047!cell wall organization and biogenesis!0.0325618814526327!27159$GO:0044247!cellular polysaccharide catabolic process!0.0325618814526327!27159$GO:0000272!polysaccharide catabolic process!0.0325618814526327!27159$GO:0045229!external encapsulating structure organization and biogenesis!0.03300816015487!27159$GO:0030246!carbohydrate binding!0.0366394871563165!27159;8547$GO:0008320!protein transmembrane transporter activity!0.0394364418177486!2$GO:0007585!respiratory gaseous exchange!0.0396389005349773!6439$GO:0006044!N-acetylglucosamine metabolic process!0.0416574366362695!27159$GO:0006041!glucosamine metabolic process!0.0416574366362695!27159$GO:0048545!response to steroid hormone stimulus!0.0416574366362695!2$GO:0042221!response to chemical stimulus!0.0416574366362695!27159;2$GO:0019956!chemokine binding!0.0416574366362695!2$GO:0019965!interleukin binding!0.0416574366362695!2$GO:0006040!amino sugar metabolic process!0.0416574366362695!27159$GO:0051260!protein homooligomerization!0.0416574366362695!2$GO:0007584!response to nutrient!0.0416574366362695!2$GO:0010035!response to inorganic substance!0.0416574366362695!2$GO:0045028!purinergic nucleotide receptor activity, G-protein coupled!0.0416574366362695!9934$GO:0001608!nucleotide receptor activity, G-protein coupled!0.0416574366362695!9934$GO:0009605!response to external stimulus!0.0416574366362695!177;2$GO:0016502!nucleotide receptor activity!0.0416574366362695!9934$GO:0001614!purinergic nucleotide receptor activity!0.0416574366362695!9934
|gostat_on_coexpression_clusters=GO:0001101!response to acid!0.0102944784231565!27159$GO:0010383!cell wall polysaccharide metabolic process!0.0102944784231565!27159$GO:0006037!cell wall chitin metabolic process!0.0102944784231565!27159$GO:0010037!response to carbon dioxide!0.0102944784231565!2$GO:0005615!extracellular space!0.0102944784231565!27159;6439;8547$GO:0045029!UDP-activated nucleotide receptor activity!0.0155385513714468!9934$GO:0019959!interleukin-8 binding!0.0155385513714468!2$GO:0015065!uridine nucleotide receptor activity!0.0155385513714468!9934$GO:0017114!wide-spectrum protease inhibitor activity!0.0155385513714468!2$GO:0050828!regulation of liquid surface tension!0.0209143579160127!6439$GO:0008061!chitin binding!0.0209143579160127!27159$GO:0044421!extracellular region part!0.0209143579160127!27159;6439;8547$GO:0043120!tumor necrosis factor binding!0.0279299039569851!2$GO:0019966!interleukin-1 binding!0.0279299039569851!2$GO:0051384!response to glucocorticoid stimulus!0.0279299039569851!2$GO:0019958!C-X-C chemokine binding!0.0279299039569851!2$GO:0003796!lysozyme activity!0.0279299039569851!27159$GO:0031960!response to corticosteroid stimulus!0.0279299039569851!2$GO:0005529!sugar binding!0.0279299039569851!27159;8547$GO:0006032!chitin catabolic process!0.0279299039569851!27159$GO:0006046!N-acetylglucosamine catabolic process!0.0279299039569851!27159$GO:0006043!glucosamine catabolic process!0.0279299039569851!27159$GO:0046348!amino sugar catabolic process!0.0279299039569851!27159$GO:0006030!chitin metabolic process!0.0279299039569851!27159$GO:0004568!chitinase activity!0.0279299039569851!27159$GO:0009620!response to fungus!0.0325618814526327!27159$GO:0010382!cell wall metabolic process!0.0325618814526327!27159$GO:0007047!cell wall organization and biogenesis!0.0325618814526327!27159$GO:0044247!cellular polysaccharide catabolic process!0.0325618814526327!27159$GO:0000272!polysaccharide catabolic process!0.0325618814526327!27159$GO:0045229!external encapsulating structure organization and biogenesis!0.03300816015487!27159$GO:0030246!carbohydrate binding!0.0366394871563165!27159;8547$GO:0008320!protein transmembrane transporter activity!0.0394364418177486!2$GO:0007585!respiratory gaseous exchange!0.0396389005349773!6439$GO:0006044!N-acetylglucosamine metabolic process!0.0416574366362695!27159$GO:0006041!glucosamine metabolic process!0.0416574366362695!27159$GO:0048545!response to steroid hormone stimulus!0.0416574366362695!2$GO:0042221!response to chemical stimulus!0.0416574366362695!27159;2$GO:0019956!chemokine binding!0.0416574366362695!2$GO:0019965!interleukin binding!0.0416574366362695!2$GO:0006040!amino sugar metabolic process!0.0416574366362695!27159$GO:0051260!protein homooligomerization!0.0416574366362695!2$GO:0007584!response to nutrient!0.0416574366362695!2$GO:0010035!response to inorganic substance!0.0416574366362695!2$GO:0045028!purinergic nucleotide receptor activity, G-protein coupled!0.0416574366362695!9934$GO:0001608!nucleotide receptor activity, G-protein coupled!0.0416574366362695!9934$GO:0009605!response to external stimulus!0.0416574366362695!177;2$GO:0016502!nucleotide receptor activity!0.0416574366362695!9934$GO:0001614!purinergic nucleotide receptor activity!0.0416574366362695!9934

Revision as of 15:57, 12 September 2012


Full id: C308_lung_Hepatocyte_liver_thyroid_heart_left_breast



Phase1 CAGE Peaks

Hg19::chr10:123886537..123886542,+p6@TACC2
Hg19::chr10:6018826..6018842,+p@chr10:6018826..6018842
+
Hg19::chr10:6018896..6018943,+p@chr10:6018896..6018943
+
Hg19::chr10:81316736..81316741,-p@chr10:81316736..81316741
-
Hg19::chr10:81374094..81374095,+p2@AK309522
Hg19::chr11:60524339..60524341,+p3@MS4A15
Hg19::chr11:60524471..60524476,+p2@MS4A15
Hg19::chr12:40619482..40619487,-p@chr12:40619482..40619487
-
Hg19::chr12:9268765..9268779,-p8@A2M
Hg19::chr13:107279210..107279243,+p@chr13:107279210..107279243
+
Hg19::chr15:49758548..49758563,+p@chr15:49758548..49758563
+
Hg19::chr17:53800009..53800012,-p11@TMEM100
Hg19::chr17:53809407..53809415,-p6@TMEM100
Hg19::chr1:111833472..111833476,+p1@CHIA
Hg19::chr1:27701307..27701322,-p1@FCN3
Hg19::chr20:15177480..15177528,+p2@MACROD2
Hg19::chr2:85886492..85886507,+p@chr2:85886492..85886507
+
Hg19::chr2:85886640..85886647,+p@chr2:85886640..85886647
+
Hg19::chr2:85886678..85886695,+p@chr2:85886678..85886695
+
Hg19::chr2:85886680..85886695,-p@chr2:85886680..85886695
-
Hg19::chr2:85886778..85886789,-p@chr2:85886778..85886789
-
Hg19::chr2:85890569..85890576,-p24@SFTPB
Hg19::chr2:85893765..85893801,-p2@SFTPB
Hg19::chr2:85895542..85895549,-p27@SFTPB
Hg19::chr3:150966924..150966933,-p13@P2RY14
Hg19::chr3:157221357..157221365,-p15@VEPH1
Hg19::chr3:157221380..157221399,-p7@VEPH1
Hg19::chr5:1548521..1548536,+p@chr5:1548521..1548536
+
Hg19::chr5:66787065..66787072,+p@chr5:66787065..66787072
+
Hg19::chr6:11291949..11291963,+p@chr6:11291949..11291963
+
Hg19::chr6:30905155..30905161,-p@chr6:30905155..30905161
-
Hg19::chr6:30905176..30905181,-p@chr6:30905176..30905181
-
Hg19::chr6:30905248..30905256,-p@chr6:30905248..30905256
-
Hg19::chr6:32152003..32152016,-p2@AGER
Hg19::chr6:32152020..32152040,-p1@AGER
Hg19::chr6:32152064..32152075,-p3@AGER
Hg19::chr6:41712177..41712188,-p@chr6:41712177..41712188
-
Hg19::chr6:41712545..41712551,-p@chr6:41712545..41712551
-
Hg19::chr8:69243711..69243722,-p4@LOC286189


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

GO IDGO nameFDR corrected p-value
GO:0001101response to acid0.0102944784231565
GO:0010383cell wall polysaccharide metabolic process0.0102944784231565
GO:0006037cell wall chitin metabolic process0.0102944784231565
GO:0010037response to carbon dioxide0.0102944784231565
GO:0005615extracellular space0.0102944784231565
GO:0045029UDP-activated nucleotide receptor activity0.0155385513714468
GO:0019959interleukin-8 binding0.0155385513714468
GO:0015065uridine nucleotide receptor activity0.0155385513714468
GO:0017114wide-spectrum protease inhibitor activity0.0155385513714468
GO:0050828regulation of liquid surface tension0.0209143579160127
GO:0008061chitin binding0.0209143579160127
GO:0044421extracellular region part0.0209143579160127
GO:0043120tumor necrosis factor binding0.0279299039569851
GO:0019966interleukin-1 binding0.0279299039569851
GO:0051384response to glucocorticoid stimulus0.0279299039569851
GO:0019958C-X-C chemokine binding0.0279299039569851
GO:0003796lysozyme activity0.0279299039569851
GO:0031960response to corticosteroid stimulus0.0279299039569851
GO:0005529sugar binding0.0279299039569851
GO:0006032chitin catabolic process0.0279299039569851
GO:0006046N-acetylglucosamine catabolic process0.0279299039569851
GO:0006043glucosamine catabolic process0.0279299039569851
GO:0046348amino sugar catabolic process0.0279299039569851
GO:0006030chitin metabolic process0.0279299039569851
GO:0004568chitinase activity0.0279299039569851
GO:0009620response to fungus0.0325618814526327
GO:0010382cell wall metabolic process0.0325618814526327
GO:0007047cell wall organization and biogenesis0.0325618814526327
GO:0044247cellular polysaccharide catabolic process0.0325618814526327
GO:0000272polysaccharide catabolic process0.0325618814526327
GO:0045229external encapsulating structure organization and biogenesis0.03300816015487
GO:0030246carbohydrate binding0.0366394871563165
GO:0008320protein transmembrane transporter activity0.0394364418177486
GO:0007585respiratory gaseous exchange0.0396389005349773
GO:0006044N-acetylglucosamine metabolic process0.0416574366362695
GO:0006041glucosamine metabolic process0.0416574366362695
GO:0048545response to steroid hormone stimulus0.0416574366362695
GO:0042221response to chemical stimulus0.0416574366362695
GO:0019956chemokine binding0.0416574366362695
GO:0019965interleukin binding0.0416574366362695
GO:0006040amino sugar metabolic process0.0416574366362695
GO:0051260protein homooligomerization0.0416574366362695
GO:0007584response to nutrient0.0416574366362695
GO:0010035response to inorganic substance0.0416574366362695
GO:0045028purinergic nucleotide receptor activity, G-protein coupled0.0416574366362695
GO:0001608nucleotide receptor activity, G-protein coupled0.0416574366362695
GO:0009605response to external stimulus0.0416574366362695
GO:0016502nucleotide receptor activity0.0416574366362695
GO:0001614purinergic nucleotide receptor activity0.0416574366362695



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 organism9.55e-30115
organ8.78e-09511
anatomical conduit1.42e-08241
anatomical cluster1.87e-08286
subdivision of digestive tract2.46e-08129
endodermal part of digestive tract2.46e-08129
abdomen element3.13e-0855
abdominal segment element3.13e-0855
abdominal segment of trunk4.59e-0861
abdomen4.59e-0861
endoderm-derived structure5.93e-08169
endoderm5.93e-08169
presumptive endoderm5.93e-08169
organ part9.48e-08219
mixed endoderm/mesoderm-derived structure1.06e-07130
digestive system1.48e-07155
digestive tract1.48e-07155
primitive gut1.48e-07155
neural tube6.33e-0757
neural rod6.33e-0757
future spinal cord6.33e-0757
neural keel6.33e-0757
gland6.62e-0759


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

No analysis results for this cluster

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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