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Coexpression cluster:C3292: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3292_optic_Mesenchymal_aorta_heart_gall_globus_penis
|id=C3292
|ontology_enrichment_celltype=CL:0000055!4.26e-09!180;CL:0000057!8.30e-08!75;CL:0000136!8.09e-07!15
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!5.58e-41!115;UBERON:0000475!5.98e-28!365;UBERON:0001049!2.31e-25!57;UBERON:0005068!2.31e-25!57;UBERON:0006241!2.31e-25!57;UBERON:0007135!2.31e-25!57;UBERON:0002616!1.78e-23!59;UBERON:0003075!9.42e-22!86;UBERON:0007284!9.42e-22!86;UBERON:0000955!1.00e-21!69;UBERON:0006238!1.00e-21!69;UBERON:0000481!1.92e-21!347;UBERON:0002346!1.20e-20!90;UBERON:0001017!2.25e-20!82;UBERON:0005743!1.76e-19!86;UBERON:0000477!3.31e-19!286;UBERON:0003080!6.06e-19!42;UBERON:0000033!1.87e-18!123;UBERON:0002780!2.18e-18!41;UBERON:0001890!2.18e-18!41;UBERON:0006240!2.18e-18!41;UBERON:0000153!4.27e-18!129;UBERON:0007811!4.27e-18!129;UBERON:0004121!1.81e-17!169;UBERON:0000073!2.30e-17!94;UBERON:0001016!2.30e-17!94;UBERON:0004111!3.93e-17!241;UBERON:0000924!5.61e-17!173;UBERON:0006601!5.61e-17!173;UBERON:0002020!2.20e-15!34;UBERON:0003528!2.20e-15!34;UBERON:0001893!3.02e-15!34;UBERON:0000025!3.12e-15!194;UBERON:0000119!5.92e-15!312;UBERON:0000468!6.19e-15!659;UBERON:0002791!8.57e-15!33;UBERON:0000483!9.77e-15!309;UBERON:0000062!1.90e-14!511;UBERON:0003056!2.48e-14!61;UBERON:0001869!5.70e-14!32;UBERON:0000064!5.08e-12!219;UBERON:0000467!1.41e-11!625;UBERON:0000480!2.71e-11!626;UBERON:0002619!6.38e-11!22;UBERON:0000956!3.14e-10!25;UBERON:0000203!3.14e-10!25;UBERON:0001950!6.82e-10!20;UBERON:0002050!2.21e-08!605;UBERON:0005423!2.21e-08!605;UBERON:0000923!3.14e-08!604;UBERON:0005291!3.14e-08!604;UBERON:0006598!3.14e-08!604;UBERON:0002532!3.14e-08!604;UBERON:0000922!4.02e-08!612;UBERON:0003076!1.34e-07!15;UBERON:0003057!1.34e-07!15;UBERON:0002308!6.90e-07!9;UBERON:0000125!6.90e-07!9
}}

Latest revision as of 12:23, 17 September 2013


Full id: C3292_optic_Mesenchymal_aorta_heart_gall_globus_penis



Phase1 CAGE Peaks

Hg19::chr12:53440813..53440830,-p1@ENST00000546566
Hg19::chr12:53440842..53440861,-p1@uc001sbj.1
Hg19::chr12:53440983..53441061,+p@chr12:53440983..53441061
+


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
fibroblast1.03e-0776
fat cell4.87e-0715
Uber Anatomy
Ontology termp-valuen
adult organism1.63e-40114
multi-tissue structure4.55e-25342
structure with developmental contribution from neural crest2.33e-24132
neural tube2.87e-2456
neural rod2.87e-2456
future spinal cord2.87e-2456
neural keel2.87e-2456
neural plate1.20e-2282
presumptive neural plate1.20e-2282
regional part of nervous system1.66e-2253
regional part of brain1.66e-2253
brain2.41e-2168
future brain2.41e-2168
neurectoderm3.84e-2186
anatomical cluster1.79e-20373
central nervous system4.33e-2081
organ system subdivision1.84e-19223
regional part of forebrain7.74e-1841
forebrain7.74e-1841
anterior neural tube7.74e-1841
future forebrain7.74e-1841
ectoderm-derived structure9.09e-18171
ectoderm9.09e-18171
presumptive ectoderm9.09e-18171
nervous system1.49e-1789
ecto-epithelium6.40e-17104
anatomical conduit4.08e-15240
brain grey matter1.15e-1434
gray matter1.15e-1434
telencephalon1.61e-1434
pre-chordal neural plate1.95e-1461
organ2.85e-14503
cell layer3.13e-14309
epithelium4.32e-14306
multi-cellular organism5.28e-14656
regional part of telencephalon1.93e-1332
tube2.16e-13192
cerebral hemisphere2.99e-1332
organ part3.51e-12218
anatomical system5.89e-12624
anatomical group1.07e-11625
regional part of cerebral cortex6.43e-1022
cerebral cortex1.78e-0925
pallium1.78e-0925
neocortex6.73e-0920
germ layer3.23e-08560
germ layer / neural crest3.23e-08560
embryonic tissue3.23e-08560
presumptive structure3.23e-08560
germ layer / neural crest derived structure3.23e-08560
epiblast (generic)3.23e-08560
embryonic structure1.02e-07564
tissue1.13e-07773
developing anatomical structure1.14e-07581
posterior neural tube1.23e-0715
chordal neural plate1.23e-0715
organism subdivision2.17e-07264
neural nucleus5.03e-079
nucleus of brain5.03e-079
embryo8.08e-07592


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)
MA0003.14.57391
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.12.37507
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.407479
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.13.21605
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.12.91906
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.12.11725
MA0146.10.707589
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.22.74132
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.21.34467
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.16.1256
MA0163.13.96434
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.29.48295
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
CCNT2#90536.336201576962630.003930750035764890.0189452029620771
CTCF#1066435.360256373075030.0064925092527670.0278674656357773
E2F1#186934.907389214879320.008460985347239390.0324099339328933
EGR1#195834.988179094810140.008056488137383440.0319466764591157
ELF1#199734.258097958807540.01295179875054610.0460625522614004
GABPB1#255337.067683836182170.002832212825417420.0153730822344873
SPI1#668838.204323508522730.001810593189410520.010890148704725
ZNF263#1012738.221841637010680.001799043925565870.0109042045465831



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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