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Coexpression cluster:C3671: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3671_Neural_Chondrocyte_hepatocellular_caudate_signet_hippocampus_papillotubular
|id=C3671
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!6.26e-36!365;UBERON:0004121!1.40e-34!169;UBERON:0000924!1.06e-33!173;UBERON:0006601!1.06e-33!173;UBERON:0000033!3.14e-33!123;UBERON:0000481!2.25e-32!347;UBERON:0000153!1.74e-31!129;UBERON:0007811!1.74e-31!129;UBERON:0005743!1.28e-30!86;UBERON:0003075!1.56e-29!86;UBERON:0007284!1.56e-29!86;UBERON:0001017!2.63e-29!82;UBERON:0000073!7.55e-29!94;UBERON:0001016!7.55e-29!94;UBERON:0001049!1.42e-28!57;UBERON:0005068!1.42e-28!57;UBERON:0006241!1.42e-28!57;UBERON:0007135!1.42e-28!57;UBERON:0002346!4.52e-28!90;UBERON:0000955!2.58e-26!69;UBERON:0006238!2.58e-26!69;UBERON:0002616!1.43e-24!59;UBERON:0003056!8.70e-23!61;UBERON:0000119!1.79e-22!312;UBERON:0000483!4.52e-22!309;UBERON:0003080!4.50e-21!42;UBERON:0002780!7.59e-21!41;UBERON:0001890!7.59e-21!41;UBERON:0006240!7.59e-21!41;UBERON:0000062!7.99e-20!511;UBERON:0004111!1.13e-19!241;UBERON:0002020!1.37e-19!34;UBERON:0003528!1.37e-19!34;UBERON:0001893!1.37e-19!34;UBERON:0002791!3.65e-19!33;UBERON:0000468!4.11e-19!659;UBERON:0000922!4.97e-19!612;UBERON:0000477!1.55e-18!286;UBERON:0001869!1.60e-18!32;UBERON:0002050!6.66e-18!605;UBERON:0005423!6.66e-18!605;UBERON:0007023!9.52e-18!115;UBERON:0000923!9.55e-18!604;UBERON:0005291!9.55e-18!604;UBERON:0006598!9.55e-18!604;UBERON:0002532!9.55e-18!604;UBERON:0000064!2.23e-17!219;UBERON:0000025!4.52e-17!194;UBERON:0000467!9.36e-17!625;UBERON:0000480!1.95e-16!626;UBERON:0000956!7.46e-15!25;UBERON:0000203!7.46e-15!25;UBERON:0002619!2.17e-13!22;UBERON:0001950!4.27e-12!20;UBERON:0004119!6.70e-10!169;UBERON:0000925!6.70e-10!169;UBERON:0006595!6.70e-10!169;UBERON:0001048!7.20e-10!168;UBERON:0001007!7.72e-09!155;UBERON:0001555!7.72e-09!155;UBERON:0007026!7.72e-09!155;UBERON:0003076!1.26e-08!15;UBERON:0003057!1.26e-08!15;UBERON:0003103!4.56e-08!69;UBERON:0005177!1.38e-07!107;UBERON:0000466!3.57e-07!126;UBERON:0003104!4.28e-07!238;UBERON:0009142!4.28e-07!238;UBERON:0001444!5.29e-07!48;UBERON:0004733!5.96e-07!12;UBERON:0002028!5.96e-07!12;UBERON:0007277!5.96e-07!12
}}

Latest revision as of 12:30, 17 September 2013


Full id: C3671_Neural_Chondrocyte_hepatocellular_caudate_signet_hippocampus_papillotubular



Phase1 CAGE Peaks

Hg19::chr17:70117153..70117174,+p1@SOX9
Hg19::chr17:70120097..70120118,+p@chr17:70120097..70120118
+
Hg19::chr17:70120252..70120370,-p@chr17:70120252..70120370
-


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure3.00e-32171
ectoderm3.00e-32171
presumptive ectoderm3.00e-32171
neural plate5.87e-3082
presumptive neural plate5.87e-3082
neural tube2.26e-2956
neural rod2.26e-2956
future spinal cord2.26e-2956
neural keel2.26e-2956
central nervous system3.75e-2981
ecto-epithelium1.43e-28104
neurectoderm2.09e-2886
anatomical cluster3.00e-28373
regional part of nervous system1.91e-2753
regional part of brain1.91e-2753
organ system subdivision3.98e-27223
nervous system1.39e-2689
multi-tissue structure1.92e-26342
brain2.62e-2668
future brain2.62e-2668
structure with developmental contribution from neural crest4.70e-26132
pre-chordal neural plate4.99e-2261
regional part of forebrain1.41e-2141
forebrain1.41e-2141
anterior neural tube1.41e-2141
future forebrain1.41e-2141
telencephalon3.48e-2034
brain grey matter3.83e-2034
gray matter3.83e-2034
regional part of telencephalon4.33e-1932
cerebral hemisphere5.38e-1932
cell layer1.37e-18309
anatomical conduit1.88e-18240
epithelium2.60e-18306
adult organism2.00e-16114
organ7.91e-16503
tube8.33e-16192
cerebral cortex1.68e-1525
pallium1.68e-1525
multi-cellular organism1.02e-14656
organ part1.48e-14218
regional part of cerebral cortex6.47e-1422
anatomical system1.55e-13624
anatomical group2.62e-13625
embryo2.64e-13592
neocortex1.38e-1220
developing anatomical structure1.90e-11581
posterior neural tube6.55e-0915
chordal neural plate6.55e-0915
embryonic structure1.07e-08564
organism subdivision2.68e-08264
germ layer2.94e-08560
germ layer / neural crest2.94e-08560
embryonic tissue2.94e-08560
presumptive structure2.94e-08560
germ layer / neural crest derived structure2.94e-08560
epiblast (generic)2.94e-08560
compound organ1.03e-0768
segmental subdivision of hindbrain4.23e-0712
hindbrain4.23e-0712
presumptive hindbrain4.23e-0712
endoderm-derived structure4.87e-07160
endoderm4.87e-07160
presumptive endoderm4.87e-07160


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)
MA0003.10.708947
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.12.13518
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
MA0073.15.1975
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.11.55117
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.11.16674
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.54885
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

No analysis results for this cluster

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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