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Coexpression cluster:C403: Difference between revisions

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|tf_chipseq_enrich=HNF4G#3174;4:4.4236034656072:0.011846833470383:0.0431556135616787
|tf_chipseq_enrich=HNF4G#3174;4:4.4236034656072:0.011846833470383:0.0431556135616787
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|tfbs_overrepresentation_for_novel_motifs=0.240292,2.34461,0.499626,0.138052,0.182732,0.137092,0.541868,1.26949,2.59267,0.398987,0.119947,0.213274,1.70198,0.523764,0.717293,0.793436,0.346619,1.25866,1.81835,1.40539,0.231339,2.79916,0.132601,0.39869,2.06982,0.22908,1.90242,0.131358,0.415824,0.753556,0.350417,0.376235,0.0971592,1.72299,0.0369069,0.465454,0.0359171,0.137767,1.22416,0.315327,0.144755,0.327908,3.48876,0.403307,1.1386,0.269598,0.184896,0.114021,0.522568,1.12448,0.239156,0.192661,0.761401,0.439939,0.572791,1.01326,0.745804,0.15794,1.36574,0.157319,0.409909,0.186447,0.902494,0.324749,0.198353,0.298136,0.652492,0.998973,0.367813,0.844111,0.31008,0.0167557,0.00194772,0.571009,0.00789256,0.383457,3.14368,0.83793,0.365188,0.082472,0.145915,0.865542,0.198116,0.192322,0.525521,0.0344222,0.00112712,0.0745059,1.31981,1.09502,0.738491,0.501948,0.389962,0.10329,0.0488346,0.114934,0.0498554,0.425289,0.261356,0.257102,0.535827,0.385331,0.420622,0.349541,0.787716,0.117458,0.336968,1.58202,0.0852584,0.376383,0.245012,0.41831,0.224609,0.394894,0.694065,0.141384,0.00912175,0.348743,0.296351,1.13513,0.563638,0.256203,0.135489,0.205724,0.797035,0.312191,0.180055,0.394066,0.601752,2.63163,2.1694,0.71864,0.61471,0.203467,0.750477,0.0678451,0.104999,1.32506,0.711091,1.54156,1.14596,0.676716,1.02356,1.08231,0.29071,0.152756,0.762167,1.3843,1.10373,0.247334,1.51557,0.000341566,0.50288,0.0650746,0.546572,0.873115,0.688707,0.0436596,0.0854065,0.916222,0.675601,0.486836,0.955853,0.256244,0.30298,0.197587,0.431755,0.183316,3.66651
}}
}}

Revision as of 14:11, 26 November 2012


Full id: C403_small_Neutrophils_temporal_leiomyoma_Hair_colon_pancreas



Phase1 CAGE Peaks

Hg19::chr15:90333754..90333771,-p@chr15:90333754..90333771
-
Hg19::chr15:90334271..90334330,-p@chr15:90334271..90334330
-
Hg19::chr15:90335468..90335503,-p@chr15:90335468..90335503
-
Hg19::chr15:90335773..90335792,-p@chr15:90335773..90335792
-
Hg19::chr15:90336331..90336350,-p20@ANPEP
Hg19::chr15:90340830..90340881,-p@chr15:90340830..90340881
-
Hg19::chr15:90344690..90344735,-p@chr15:90344690..90344735
-
Hg19::chr15:90344759..90344769,-p@chr15:90344759..90344769
-
Hg19::chr15:90346462..90346504,+p@chr15:90346462..90346504
+
Hg19::chr15:90346527..90346545,-p@chr15:90346527..90346545
-
Hg19::chr15:90346711..90346744,-p@chr15:90346711..90346744
-
Hg19::chr15:90346918..90346991,-p@chr15:90346918..90346991
-
Hg19::chr15:90347171..90347214,-p8@ANPEP
Hg19::chr15:90347564..90347578,-p15@ANPEP
Hg19::chr15:90347748..90347765,-p19@ANPEP
Hg19::chr15:90347792..90347817,-p6@ANPEP
Hg19::chr15:90348382..90348416,-p16@ANPEP
Hg19::chr15:90348639..90348671,-p12@ANPEP
Hg19::chr15:90348673..90348697,-p11@ANPEP
Hg19::chr15:90349254..90349268,-p@chr15:90349254..90349268
-
Hg19::chr15:90349462..90349473,-p11@AB462940
Hg19::chr15:90349509..90349523,-p7@AB462940
Hg19::chr15:90349753..90349762,-p9@AB462940
Hg19::chr15:90349765..90349774,-p10@AB462940
Hg19::chr15:90349797..90349814,-p3@AB462940
Hg19::chr15:90349899..90349910,-p14@ANPEP


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:0016284alanine aminopeptidase activity0.02320538482672
GO:0004179membrane alanyl aminopeptidase activity0.02320538482672
GO:0005793ER-Golgi intermediate compartment0.02320538482672
GO:0004177aminopeptidase activity0.0268750735900153
GO:0008235metalloexopeptidase activity0.0268750735900153
GO:0001525angiogenesis0.0268750735900153
GO:0048514blood vessel morphogenesis0.0268750735900153
GO:0048646anatomical structure formation0.0268750735900153
GO:0001568blood vessel development0.0268750735900153
GO:0001944vasculature development0.0268750735900153
GO:0008238exopeptidase activity0.0275226657247145
GO:0042277peptide binding0.0280623258369638
GO:0005625soluble fraction0.0291416460614624
GO:0009887organ morphogenesis0.0406903724635975
GO:0008237metallopeptidase activity0.0406903724635975



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
multi fate stem cell9.96e-28427
somatic stem cell1.90e-26433
stem cell8.34e-25441
somatic cell7.59e-20588
connective tissue cell9.34e-19361
fibroblast3.03e-1776
mesenchymal cell2.27e-16354
defensive cell7.44e-1648
phagocyte7.44e-1648
classical monocyte3.55e-1442
CD14-positive, CD16-negative classical monocyte3.55e-1442
muscle precursor cell3.00e-1358
myoblast3.00e-1358
multi-potent skeletal muscle stem cell3.00e-1358
motile cell1.57e-12386
monopoietic cell1.63e-1259
monocyte1.63e-1259
monoblast1.63e-1259
promonocyte1.63e-1259
skin fibroblast3.98e-1223
myeloid leukocyte6.26e-1272
macrophage dendritic cell progenitor1.15e-1161
contractile cell1.93e-1159
muscle cell1.94e-1155
myeloid lineage restricted progenitor cell7.93e-1166
granulocyte monocyte progenitor cell1.81e-1067
animal cell7.58e-10679
eukaryotic cell7.58e-10679
smooth muscle cell1.64e-0943
smooth muscle myoblast1.64e-0943
electrically responsive cell4.02e-0961
electrically active cell4.02e-0961
stuff accumulating cell2.04e-0787
vascular associated smooth muscle cell4.36e-0732
mesenchymal stem cell of adipose8.07e-078
Uber Anatomy
Ontology termp-valuen
musculoskeletal system6.52e-24167
connective tissue7.38e-18371
mesoderm9.40e-18315
mesoderm-derived structure9.40e-18315
presumptive mesoderm9.40e-18315
somite8.96e-1771
presomitic mesoderm8.96e-1771
presumptive segmental plate8.96e-1771
dermomyotome8.96e-1771
trunk paraxial mesoderm8.96e-1771
paraxial mesoderm2.73e-1672
presumptive paraxial mesoderm2.73e-1672
dense mesenchyme tissue8.01e-1673
epithelial vesicle2.85e-1578
multilaminar epithelium2.23e-1383
muscle tissue9.23e-1264
musculature9.23e-1264
musculature of body9.23e-1264
skeletal muscle tissue1.68e-1162
striated muscle tissue1.68e-1162
myotome1.68e-1162
trunk mesenchyme2.26e-11122
bone marrow5.55e-1176
integument1.21e-1046
integumental system1.21e-1046
skeletal system1.52e-10100
skeletal element5.97e-1090
mesenchyme2.26e-09160
entire embryonic mesenchyme2.26e-09160
unilaminar epithelium3.17e-09148
bone element3.83e-0982
lateral plate mesoderm5.10e-09203
skin of body9.13e-0941
artery1.72e-0842
arterial blood vessel1.72e-0842
arterial system1.72e-0842
dermis2.81e-089
dermatome2.81e-089
future dermis2.81e-089
immune system8.96e-0893
hematopoietic system1.22e-0798
blood island1.22e-0798
systemic artery1.27e-0733
systemic arterial system1.27e-0733
hemolymphoid system8.36e-07108
tissue9.10e-07773


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
HNF4G#317444.42360346560720.0118468334703830.0431556135616787



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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