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Coexpression cluster:C2925: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2925_optic_smooth_colon_corpus_globus_thalamus_ductus
|id=C2925
|ontology_enrichment_celltype=CL:0002139!9.28e-12!24;CL:0000115!8.04e-11!35;CL:0000071!1.90e-09!18;CL:0002546!1.90e-09!18;CL:0002078!2.43e-09!44;CL:0000213!9.35e-07!57;CL:0000215!9.35e-07!57
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.75e-38!115;UBERON:0000477!3.77e-22!286;UBERON:0004111!1.96e-18!241;UBERON:0000481!6.87e-18!347;UBERON:0001049!6.70e-16!57;UBERON:0005068!6.70e-16!57;UBERON:0006241!6.70e-16!57;UBERON:0007135!6.70e-16!57;UBERON:0002346!6.86e-16!90;UBERON:0000468!2.08e-15!659;UBERON:0003075!4.99e-15!86;UBERON:0007284!4.99e-15!86;UBERON:0002616!6.82e-15!59;UBERON:0000119!1.52e-14!312;UBERON:0000483!3.84e-14!309;UBERON:0000025!7.84e-14!194;UBERON:0000467!1.42e-13!625;UBERON:0000480!2.61e-13!626;UBERON:0002020!4.20e-13!34;UBERON:0003528!4.20e-13!34;UBERON:0001893!5.00e-13!34;UBERON:0002791!1.37e-12!33;UBERON:0003080!2.21e-12!42;UBERON:0002780!2.32e-12!41;UBERON:0001890!2.32e-12!41;UBERON:0006240!2.32e-12!41;UBERON:0005743!5.78e-12!86;UBERON:0000033!6.07e-12!123;UBERON:0000922!7.38e-12!612;UBERON:0001869!9.11e-12!32;UBERON:0000073!1.57e-11!94;UBERON:0001016!1.57e-11!94;UBERON:0000955!1.63e-11!69;UBERON:0006238!1.63e-11!69;UBERON:0000153!2.67e-11!129;UBERON:0007811!2.67e-11!129;UBERON:0002050!6.47e-11!605;UBERON:0005423!6.47e-11!605;UBERON:0001017!6.72e-11!82;UBERON:0000475!8.65e-11!365;UBERON:0000923!1.24e-10!604;UBERON:0005291!1.24e-10!604;UBERON:0006598!1.24e-10!604;UBERON:0002532!1.24e-10!604;UBERON:0003056!1.47e-10!61;UBERON:0000064!1.97e-10!219;UBERON:0000924!8.68e-10!173;UBERON:0006601!8.68e-10!173;UBERON:0001986!1.90e-09!18;UBERON:0004638!1.90e-09!18;UBERON:0004852!1.90e-09!18;UBERON:0004121!4.08e-09!169;UBERON:0000956!2.05e-08!25;UBERON:0000203!2.05e-08!25;UBERON:0000062!2.30e-08!511;UBERON:0002619!3.23e-08!22;UBERON:0004921!1.12e-07!129;UBERON:0004185!1.12e-07!129;UBERON:0001007!1.53e-07!155;UBERON:0001555!1.53e-07!155;UBERON:0007026!1.53e-07!155;UBERON:0001950!1.78e-07!20;UBERON:0000487!1.93e-07!22;UBERON:0006914!4.12e-07!25
}}

Latest revision as of 12:15, 17 September 2013


Full id: C2925_optic_smooth_colon_corpus_globus_thalamus_ductus



Phase1 CAGE Peaks

Hg19::chr8:38614412..38614456,+p7@TACC1
Hg19::chr8:38614754..38614774,+p13@TACC1
Hg19::chr8:38614778..38614806,+p5@TACC1
Hg19::chr8:38614807..38614824,+p10@TACC1


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>

Uber Anatomy
Ontology termp-valuen
adult organism6.34e-38114
anatomical cluster1.43e-26373
multi-tissue structure2.78e-20342
anatomical conduit3.19e-19240
organ system subdivision6.59e-19223
neurectoderm9.24e-1786
neural tube1.63e-1656
neural rod1.63e-1656
future spinal cord1.63e-1656
neural keel1.63e-1656
neural plate8.48e-1682
presumptive neural plate8.48e-1682
structure with developmental contribution from neural crest1.00e-15132
regional part of nervous system3.23e-1553
regional part of brain3.23e-1553
multi-cellular organism4.74e-15656
cell layer9.92e-15309
epithelium2.97e-14306
tube3.45e-14192
anatomical system1.53e-13624
brain grey matter1.75e-1334
gray matter1.75e-1334
telencephalon2.02e-1334
anatomical group2.74e-13625
regional part of forebrain1.39e-1241
forebrain1.39e-1241
anterior neural tube1.39e-1241
future forebrain1.39e-1241
regional part of telencephalon2.63e-1232
cerebral hemisphere3.88e-1232
brain1.23e-1168
future brain1.23e-1168
central nervous system2.85e-1181
nervous system6.58e-1189
pre-chordal neural plate6.85e-1161
embryo1.26e-10592
organ part2.23e-10218
ecto-epithelium2.97e-10104
ectoderm-derived structure1.25e-09171
ectoderm1.25e-09171
presumptive ectoderm1.25e-09171
developing anatomical structure2.05e-09581
embryonic structure4.85e-09564
blood vessel endothelium5.19e-0918
endothelium5.19e-0918
cardiovascular system endothelium5.19e-0918
germ layer5.65e-09560
germ layer / neural crest5.65e-09560
embryonic tissue5.65e-09560
presumptive structure5.65e-09560
germ layer / neural crest derived structure5.65e-09560
epiblast (generic)5.65e-09560
cerebral cortex1.64e-0825
pallium1.64e-0825
regional part of cerebral cortex2.09e-0822
neocortex1.16e-0720
subdivision of digestive tract1.32e-07118
digestive system1.71e-07145
digestive tract1.71e-07145
primitive gut1.71e-07145
simple squamous epithelium3.44e-0722
organ5.38e-07503
squamous epithelium6.90e-0725
neural nucleus6.92e-079
nucleus of brain6.92e-079


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)
MA0003.15.41581
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.86845
MA0017.10.577281
MA0019.13.35236
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.14.01633
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.13.33774
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.13.89719
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.11.29536
MA0105.11.90157
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.12.01976
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.12.17614
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.11.63368
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.12.31379
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.24.29465
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.13.48623
MA0155.12.30186
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.24.91669
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
MA0442.10



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#1066445.360256373075030.001211145381643620.00820303583096487
E2F1#186944.907389214879320.001724022357361790.0106851326912651
EBF1#187936.679850134926750.005184294118278910.0240651803821917
HNF4A#3172423.13229036295373.48990320893214e-060.000115966274654045



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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