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Coexpression cluster:C381: Difference between revisions

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|tf_chipseq_enrich=FOS#2353;23:7.39117757516326:6.28380072586658e-18:1.38162918738691e-15!GATA2#2624;15:6.82764200011821:3.63335374939682e-10:3.62776130242117e-08!JUN#3725;10:4.46886756869155:3.6106115242246e-05:0.000698829979574672
|tf_chipseq_enrich=FOS#2353;23:7.39117757516326:6.28380072586658e-18:1.38162918738691e-15!GATA2#2624;15:6.82764200011821:3.63335374939682e-10:3.62776130242117e-08!JUN#3725;10:4.46886756869155:3.6106115242246e-05:0.000698829979574672
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|tfbs_overrepresentation_for_novel_motifs=0.211017,0.846994,0.202592,0.388836,0.157597,0.121944,0.166546,0.156756,0.308585,0.0128145,0.105867,0.194352,2.8182,0.159448,0.156208,0.180739,0.864397,2.52825,0.00758457,0.118168,0.05516,0.0965726,0.117723,0.152436,0.256819,1.13568,0.0249841,0.116555,0.36738,0.434267,0.0948604,0.352308,0.204444,1.18698,0.0302015,0.355517,0.0293368,0.122579,0.467484,0.0464435,0.122849,0.293556,0.12203,3.01395,0.0547788,0.512818,0.167225,0.100336,0.287765,0.0415313,0.219219,0.174632,0.447734,0.414705,0.545525,0.161247,0.376071,0.141618,0.648178,0.14103,0.385258,0.168703,0.153907,0.302097,0.180069,0.276238,0.62433,0.968521,0.34408,0.814438,0.276665,0.553638,0.00883858,0.543765,0.0317128,0.758576,0.152757,0.787568,0.341516,0.908192,0.0422391,0.30128,0.179843,0.542977,0.49889,0.000134547,0.0203918,2.26003,0.237365,1.06421,0.709557,0.475666,0.36573,0.414815,0.158355,0.450781,1.2521,0.400332,0.240628,0.537629,0.101994,0.361201,0.395756,0.870771,1.356,0.103543,0.843302,0.157343,0.256507,0.141721,0.215431,0.39349,0.761074,0.110777,0.665507,0.28674,0.0154366,0.646865,0.274506,1.01913,0.536488,2.6921,0.120436,0.18712,0.767667,0.289886,0.489153,0.369745,0.574137,0.239526,0.476257,0.0962711,6.10968,1.03875,0.721448,0.387663,1.06149,0.373297,0.682384,1.50986,1.115,0.648318,0.952311,0.397438,0.269036,0.838665,0.713342,1.35281,1.01503,0.0184789,0.00692196,0.000197059,0.476584,0.142269,0.971704,0.843272,0.641569,0.334165,0.256891,0.0617651,0.647214,0.460792,0.340895,0.225949,0.28094,0.179337,0.19156,0.496807,0.02208
}}
}}

Revision as of 14:10, 26 November 2012


Full id: C381_Endothelial_Renal_Hepatic_Lymphatic_Fibroblast_squamous_esophagus



Phase1 CAGE Peaks

Hg19::chr10:50153703..50153720,+p7@WDFY4
Hg19::chr10:50153735..50153750,+p6@WDFY4
Hg19::chr11:19138741..19138756,+p2@ZDHHC13
Hg19::chr12:105863636..105863650,+p@chr12:105863636..105863650
+
Hg19::chr12:105863654..105863682,+p@chr12:105863654..105863682
+
Hg19::chr12:105863705..105863718,+p@chr12:105863705..105863718
+
Hg19::chr12:118112251..118112272,-p12@KSR2
Hg19::chr12:96830430..96830450,+p@chr12:96830430..96830450
+
Hg19::chr13:32835894..32835907,+p@chr13:32835894..32835907
+
Hg19::chr13:32835912..32835936,+p@chr13:32835912..32835936
+
Hg19::chr13:32838801..32838818,+p9@FRY
Hg19::chr13:32838839..32838850,+p20@FRY
Hg19::chr15:39423060..39423066,+p@chr15:39423060..39423066
+
Hg19::chr15:39542867..39542890,+p1@C15orf54
Hg19::chr18:33046982..33046991,-p@chr18:33046982..33046991
-
Hg19::chr18:33047039..33047063,-p@chr18:33047039..33047063
-
Hg19::chr18:33047076..33047099,-p@chr18:33047076..33047099
-
Hg19::chr18:33047117..33047138,-p@chr18:33047117..33047138
-
Hg19::chr18:33047157..33047168,-p@chr18:33047157..33047168
-
Hg19::chr2:216713591..216713606,-p@chr2:216713591..216713606
-
Hg19::chr2:56216687..56216727,-p1@MIR216A
Hg19::chr2:56216738..56216739,-p@chr2:56216738..56216739
-
Hg19::chr4:11545590..11545602,+p@chr4:11545590..11545602
+
Hg19::chr5:71853090..71853107,+p@chr5:71853090..71853107
+
Hg19::chr5:95920642..95920681,+p1@ENST00000513158
Hg19::chr7:106720036..106720059,-p@chr7:106720036..106720059
-
Hg19::chr7:139741594..139741615,-p5@PARP12
Hg19::chrX:15518894..15518905,+p2@BMX


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
endothelial cell of vascular tree4.71e-13624
endothelial cell1.58e-13036
meso-epithelial cell2.42e-10345
blood vessel endothelial cell3.17e-10318
embryonic blood vessel endothelial progenitor cell3.17e-10318
lining cell5.90e-7958
barrier cell5.90e-7958
endothelial cell of artery4.44e-529
mesodermal cell1.35e-37121
vein endothelial cell4.09e-366
aortic endothelial cell1.42e-356
lymphangioblast1.25e-336
endothelial cell of lymphatic vessel1.25e-336
vascular lymphangioblast1.25e-336
squamous epithelial cell1.03e-2663
endothelial cell of umbilical vein3.98e-193
capillary endothelial cell6.73e-183
embryonic cell5.06e-15250
epithelial cell1.03e-13253
thoracic aorta endothelial cell5.96e-132
endothelial cell of sinusoid3.84e-122
endothelial cell of hepatic sinusoid3.84e-122
fenestrated cell9.56e-115
glomerular endothelial cell9.56e-115
glomerular cell8.26e-087
kidney corpuscule cell8.26e-087
Uber Anatomy
Ontology termp-valuen
blood vessel endothelium3.17e-10318
endothelium3.17e-10318
cardiovascular system endothelium3.17e-10318
simple squamous epithelium9.18e-8422
squamous epithelium2.99e-7325
vessel3.32e-5768
endothelial tube4.44e-529
arterial system endothelium4.44e-529
endothelium of artery4.44e-529
vasculature3.49e-4978
vascular system3.49e-4978
epithelial tube open at both ends1.68e-3959
blood vessel1.68e-3959
blood vasculature1.68e-3959
vascular cord1.68e-3959
cardiovascular system3.06e-39109
circulatory system4.88e-38112
splanchnic layer of lateral plate mesoderm2.06e-3283
epithelial tube2.42e-28117
lymphatic vessel4.10e-258
lymph vasculature4.10e-258
lymphatic part of lymphoid system4.10e-258
vein6.59e-249
venous blood vessel6.59e-249
venous system6.59e-249
lymphoid system5.37e-2010
anatomical conduit9.38e-19240
microcirculatory vessel6.73e-183
endothelium of capillary6.73e-183
capillary6.73e-183
tube4.52e-15192
unilaminar epithelium1.69e-14148
lateral plate mesoderm5.73e-14203
segment of aorta5.96e-132
thoracic aorta5.96e-132
artery3.14e-1242
arterial blood vessel3.14e-1242
arterial system3.14e-1242
hepatic sinusoid3.84e-122
abdomen blood vessel3.84e-122
sinusoid3.84e-122
abdominal segment blood vessel3.84e-122
umbilical vein1.12e-115
umbilical blood vessel8.31e-119
anatomical cluster1.06e-10373
aorta9.19e-1021
aortic system9.19e-1021
parenchyma3.40e-0915
mesoderm8.92e-09315
mesoderm-derived structure8.92e-09315
presumptive mesoderm8.92e-09315
liver parenchyma2.19e-083
liver lobule2.19e-083
hepatic duct2.19e-083
epithelium2.54e-08306
cell layer3.46e-08309
primitive nephron8.26e-087
renal glomerulus8.26e-087
renal corpuscle8.26e-087
glomerular capsule8.26e-087
metanephric mesenchyme8.26e-087
glomerular tuft8.26e-087
S-shaped body8.26e-087
renal vesicle8.26e-087
comma-shaped body8.26e-087
duct3.28e-0719
mesonephric epithelium6.91e-078
mesonephric tubule6.91e-078
nephric duct6.91e-078
renal duct6.91e-078
mesonephric duct6.91e-078
pronephric duct6.91e-078


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
FOS#2353237.391177575163266.28380072586658e-181.38162918738691e-15
GATA2#2624156.827642000118213.63335374939682e-103.62776130242117e-08
JUN#3725104.468867568691553.6106115242246e-050.000698829979574672



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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