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Coexpression cluster:C2318: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2318_extraskeletal_adrenal_Lymphatic_Endothelial_leiomyoblastoma_Preadipocyte_occipital
|id=C2318
|ontology_enrichment_celltype=CL:0000055!3.68e-14!180;CL:0000220!9.62e-13!246;CL:0002321!1.97e-12!248;CL:0000057!3.13e-12!75;CL:0000222!2.90e-11!119;CL:0002139!4.26e-11!24;CL:0000213!1.87e-10!57;CL:0000215!1.87e-10!57;CL:0000115!2.07e-09!35;CL:0002078!3.94e-08!44;CL:0000071!2.41e-07!18;CL:0002546!2.41e-07!18;CL:0000076!4.54e-07!62
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!2.28e-22!659;UBERON:0000475!5.56e-19!365;UBERON:0000924!2.69e-18!173;UBERON:0006601!2.69e-18!173;UBERON:0000119!2.62e-17!312;UBERON:0000483!8.77e-17!309;UBERON:0004121!1.72e-16!169;UBERON:0000467!3.77e-16!625;UBERON:0000480!7.60e-16!626;UBERON:0000477!4.53e-15!286;UBERON:0000033!6.15e-15!123;UBERON:0000153!2.65e-14!129;UBERON:0007811!2.65e-14!129;UBERON:0000922!1.95e-13!612;UBERON:0002050!1.04e-12!605;UBERON:0005423!1.04e-12!605;UBERON:0002049!1.06e-12!79;UBERON:0007798!1.06e-12!79;UBERON:0004111!1.11e-12!241;UBERON:0000923!1.52e-12!604;UBERON:0005291!1.52e-12!604;UBERON:0006598!1.52e-12!604;UBERON:0002532!1.52e-12!604;UBERON:0000481!2.93e-12!347;UBERON:0000055!4.79e-10!69;UBERON:0004872!5.48e-10!84;UBERON:0002346!7.25e-10!90;UBERON:0001950!1.24e-09!20;UBERON:0003102!1.45e-09!95;UBERON:0002619!1.83e-09!22;UBERON:0003056!4.56e-09!61;UBERON:0005743!4.62e-09!86;UBERON:0001869!1.33e-08!32;UBERON:0000073!1.66e-08!94;UBERON:0001016!1.66e-08!94;UBERON:0000025!2.20e-08!194;UBERON:0004535!2.34e-08!110;UBERON:0001893!2.77e-08!34;UBERON:0003075!2.93e-08!86;UBERON:0007284!2.93e-08!86;UBERON:0000956!4.93e-08!25;UBERON:0000203!4.93e-08!25;UBERON:0000064!5.44e-08!219;UBERON:0001444!6.11e-08!48;UBERON:0001009!6.62e-08!113;UBERON:0002791!6.76e-08!33;UBERON:0001981!8.65e-08!60;UBERON:0007500!8.65e-08!60;UBERON:0004537!8.65e-08!60;UBERON:0006965!8.65e-08!60;UBERON:0001017!9.06e-08!82;UBERON:0002020!1.16e-07!34;UBERON:0003528!1.16e-07!34;UBERON:0001986!2.41e-07!18;UBERON:0004638!2.41e-07!18;UBERON:0004852!2.41e-07!18;UBERON:0000486!3.28e-07!82;UBERON:0002780!4.65e-07!41;UBERON:0001890!4.65e-07!41;UBERON:0006240!4.65e-07!41;UBERON:0003080!5.54e-07!42;UBERON:0000955!6.93e-07!69;UBERON:0006238!6.93e-07!69;UBERON:0002097!7.09e-07!40
}}

Latest revision as of 12:03, 17 September 2013


Full id: C2318_extraskeletal_adrenal_Lymphatic_Endothelial_leiomyoblastoma_Preadipocyte_occipital



Phase1 CAGE Peaks

Hg19::chr14:85996451..85996468,+p2@FLRT2
Hg19::chr14:85996471..85996497,+p1@FLRT2
Hg19::chr14:85996507..85996521,+p3@FLRT2
Hg19::chr14:85999686..85999701,+p@chr14:85999686..85999701
+


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
anatomical cluster3.33e-22373
multi-cellular organism5.31e-22656
ectoderm-derived structure5.72e-19171
ectoderm5.72e-19171
presumptive ectoderm5.72e-19171
cell layer1.10e-17309
epithelium3.85e-17306
anatomical system5.60e-16624
anatomical group1.10e-15625
embryonic structure2.04e-14564
multi-tissue structure6.65e-14342
structure with developmental contribution from neural crest7.40e-14132
germ layer2.30e-13560
germ layer / neural crest2.30e-13560
embryonic tissue2.30e-13560
presumptive structure2.30e-13560
germ layer / neural crest derived structure2.30e-13560
epiblast (generic)2.30e-13560
vasculature3.38e-1378
vascular system3.38e-1378
anatomical conduit7.22e-13240
developing anatomical structure7.96e-13581
embryo1.62e-12592
ecto-epithelium6.33e-12104
vessel1.61e-1068
surface structure1.72e-1099
splanchnic layer of lateral plate mesoderm3.26e-1083
neocortex9.39e-1020
neurectoderm1.11e-0986
regional part of cerebral cortex1.60e-0922
pre-chordal neural plate5.74e-0961
cerebral hemisphere7.70e-0932
cardiovascular system1.14e-08109
telencephalon1.83e-0834
tube1.97e-08192
epithelial tube open at both ends2.75e-0859
blood vessel2.75e-0859
blood vasculature2.75e-0859
vascular cord2.75e-0859
regional part of telencephalon2.84e-0832
organ part3.53e-08218
cerebral cortex3.82e-0825
pallium3.82e-0825
circulatory system3.85e-08112
neural plate4.63e-0882
presumptive neural plate4.63e-0882
central nervous system6.13e-0881
blood vessel endothelium6.84e-0818
endothelium6.84e-0818
cardiovascular system endothelium6.84e-0818
brain grey matter7.14e-0834
gray matter7.14e-0834
head9.16e-0856
nervous system1.62e-0789
skin of body2.29e-0741
subdivision of head2.61e-0749
multilaminar epithelium2.61e-0783
regional part of forebrain3.64e-0741
forebrain3.64e-0741
anterior neural tube3.64e-0741
future forebrain3.64e-0741
brain4.08e-0768
future brain4.08e-0768
squamous epithelium4.45e-0725
anterior region of body4.48e-0762
craniocervical region4.48e-0762
organism subdivision6.62e-07264
integument7.24e-0746
integumental system7.24e-0746


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)
MA0003.10.720743
MA0004.11.69588
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
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
MA0055.10.396851
MA0056.10
MA0057.11.28333
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.11.92841
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.214613
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.12.13662
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.12.27878
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.12.66544
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.11.43218
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.221129
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.98779
MA0137.21.37305
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.21162
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.06783
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.657636
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
GATA2#262439.55869880016550.001818151618357440.0108954519663549
MAX#414934.839416631755340.01315737137836840.0466079676215247
ZNF263#1012748.221841637010680.0002187871180958320.00248368563334898



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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