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Coexpression cluster:C1478: Difference between revisions

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}}
}}

Revision as of 19:57, 22 January 2013


Full id: C1478_nonsmall_smallcell_small_pineal_cerebellum_argyrophil_gastrointestinal



Phase1 CAGE Peaks

Hg19::chr20:20350223..20350235,-p@chr20:20350223..20350235
-
Hg19::chr8:53161967..53161974,-p11@ST18
Hg19::chr8:53162019..53162028,-p12@ST18
Hg19::chr8:53162037..53162058,-p5@ST18
Hg19::chr8:53166899..53166914,-p3@ST18
Hg19::chr8:53166916..53166925,-p10@ST18


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
neural tube6.20e-4156
neural rod6.20e-4156
future spinal cord6.20e-4156
neural keel6.20e-4156
central nervous system1.52e-3981
regional part of nervous system1.94e-3753
regional part of brain1.94e-3753
nervous system4.55e-3789
brain7.68e-3268
future brain7.68e-3268
neural plate8.25e-2882
presumptive neural plate8.25e-2882
neurectoderm3.59e-2686
regional part of forebrain1.81e-2341
forebrain1.81e-2341
anterior neural tube1.81e-2341
future forebrain1.81e-2341
ecto-epithelium4.05e-22104
organ system subdivision4.16e-22223
posterior neural tube6.98e-2015
chordal neural plate6.98e-2015
adult organism8.08e-18114
ectoderm-derived structure9.02e-18171
ectoderm9.02e-18171
presumptive ectoderm9.02e-18171
diencephalon2.07e-177
future diencephalon2.07e-177
segmental subdivision of hindbrain2.19e-1612
hindbrain2.19e-1612
presumptive hindbrain2.19e-1612
pre-chordal neural plate4.11e-1661
segmental subdivision of nervous system5.11e-1513
gland of diencephalon7.71e-154
neuroendocrine gland7.71e-154
brain grey matter9.92e-1534
gray matter9.92e-1534
structure with developmental contribution from neural crest1.74e-14132
regional part of metencephalon7.77e-139
metencephalon7.77e-139
future metencephalon7.77e-139
brainstem9.63e-136
telencephalon1.34e-1234
regional part of telencephalon1.56e-1132
cerebral hemisphere1.56e-1132
small intestine1.54e-104
regional part of cerebral cortex8.55e-1022
pons1.18e-093
anatomical cluster1.36e-09373
tube1.73e-09192
neural nucleus1.16e-089
nucleus of brain1.16e-089
regional part of diencephalon1.55e-084
cerebral cortex1.78e-0825
pallium1.78e-0825
pineal body2.00e-082
regional part of epithalamus2.00e-082
secretory circumventricular organ2.00e-082
circumventricular organ2.00e-082
epithalamus2.00e-082
pituitary gland4.16e-082
corpus striatum6.02e-084
striatum6.02e-084
ventral part of telencephalon6.02e-084
future corpus striatum6.02e-084
Ammon's horn1.04e-072
lobe parts of cerebral cortex1.04e-072
hippocampal formation1.04e-072
limbic lobe1.04e-072
locus ceruleus4.69e-072
brainstem nucleus4.69e-072
hindbrain nucleus4.69e-072
anatomical conduit9.23e-07240


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)
MA0003.10.026277
MA0004.10.558729
MA0006.10.391183
MA0007.12.2901
MA0009.11.03681
MA0014.10.108006
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.11.41501
MA0042.11.3446
MA0043.11.03713
MA0046.11.02569
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0214749
MA0074.10.660398
MA0076.10.475586
MA0077.13.73767
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.993014
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.865577
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.11.50842
MA0141.10.455728
MA0142.10.838805
MA0143.11.72302
MA0144.10.299851
MA0145.10.107156
MA0146.10.232472
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.21.50688
MA0039.20.00570825
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.10.0961854
MA0156.11.07131
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.150673
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.27.22997e-05
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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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