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{{Coexpression_clusters
{
|full_id=C377_pituitary_small_smallcell_cerebellum_pineal_pons_neuroblastoma

Latest revision as of 11:21, 17 September 2013


Full id: C377_pituitary_small_smallcell_cerebellum_pineal_pons_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr17:27382155..27382164,+p@chr17:27382155..27382164
+
Hg19::chr20:5892147..5892163,+p1@CHGB
Hg19::chr20:5897502..5897528,+p@chr20:5897502..5897528
+
Hg19::chr20:5903109..5903130,+p@chr20:5903109..5903130
+
Hg19::chr20:5903160..5903179,+p@chr20:5903160..5903179
+
Hg19::chr20:5903185..5903220,+p@chr20:5903185..5903220
+
Hg19::chr20:5903291..5903312,-p@chr20:5903291..5903312
-
Hg19::chr20:5903294..5903305,+p@chr20:5903294..5903305
+
Hg19::chr20:5903323..5903338,+p@chr20:5903323..5903338
+
Hg19::chr20:5903421..5903428,+p@chr20:5903421..5903428
+
Hg19::chr20:5903426..5903436,-p@chr20:5903426..5903436
-
Hg19::chr20:5903492..5903502,-p@chr20:5903492..5903502
-
Hg19::chr20:5903646..5903656,+p@chr20:5903646..5903656
+
Hg19::chr20:5903694..5903708,+p@chr20:5903694..5903708
+
Hg19::chr20:5903713..5903737,+p@chr20:5903713..5903737
+
Hg19::chr20:5903751..5903780,+p@chr20:5903751..5903780
+
Hg19::chr20:5903783..5903796,+p@chr20:5903783..5903796
+
Hg19::chr20:5903825..5903912,+p@chr20:5903825..5903912
+
Hg19::chr20:5903888..5903912,-p@chr20:5903888..5903912
-
Hg19::chr20:5903937..5903949,+p@chr20:5903937..5903949
+
Hg19::chr20:5903983..5904030,-p@chr20:5903983..5904030
-
Hg19::chr20:5904015..5904025,+p@chr20:5904015..5904025
+
Hg19::chr20:5904046..5904073,-p@chr20:5904046..5904073
-
Hg19::chr20:5904056..5904076,+p@chr20:5904056..5904076
+
Hg19::chr20:5904110..5904121,+p@chr20:5904110..5904121
+
Hg19::chr20:5904190..5904198,+p@chr20:5904190..5904198
+
Hg19::chr20:5904275..5904286,+p@chr20:5904275..5904286
+
Hg19::chr20:5904344..5904383,+p@chr20:5904344..5904383
+
Hg19::chr2:166529664..166529668,+p@chr2:166529664..166529668
+


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
regional part of nervous system4.77e-6953
regional part of brain4.77e-6953
neural tube6.75e-6956
neural rod6.75e-6956
future spinal cord6.75e-6956
neural keel6.75e-6956
brain1.02e-5768
future brain1.02e-5768
central nervous system5.70e-5381
regional part of forebrain7.24e-5241
forebrain7.24e-5241
anterior neural tube7.24e-5241
future forebrain7.24e-5241
nervous system9.48e-5089
neural plate4.01e-4782
presumptive neural plate4.01e-4782
neurectoderm1.59e-4486
brain grey matter1.18e-4034
gray matter1.18e-4034
telencephalon2.49e-4034
cerebral hemisphere2.91e-3932
adult organism2.64e-38114
regional part of cerebral cortex1.13e-3722
ecto-epithelium1.93e-37104
pre-chordal neural plate1.76e-3561
regional part of telencephalon2.26e-3532
cerebral cortex7.87e-3325
pallium7.87e-3325
neocortex5.22e-3220
structure with developmental contribution from neural crest1.54e-29132
ectoderm-derived structure5.27e-23171
ectoderm5.27e-23171
presumptive ectoderm5.27e-23171
organ system subdivision2.42e-22223
gyrus3.71e-206
segmental subdivision of hindbrain9.96e-1812
hindbrain9.96e-1812
presumptive hindbrain9.96e-1812
posterior neural tube2.17e-1715
chordal neural plate2.17e-1715
tube2.44e-17192
segmental subdivision of nervous system2.97e-1613
gland of diencephalon2.06e-154
neuroendocrine gland2.06e-154
brainstem3.37e-146
regional part of metencephalon4.32e-149
metencephalon4.32e-149
future metencephalon4.32e-149
diencephalon5.23e-137
future diencephalon5.23e-137
anatomical conduit6.73e-13240
temporal lobe6.11e-126
pons2.80e-113
limbic system5.09e-115
frontal cortex7.57e-113
organ part2.74e-10218
epithelium2.78e-10306
cell layer4.36e-10309
anatomical cluster6.82e-10373
neural nucleus2.56e-099
nucleus of brain2.56e-099
multi-tissue structure7.30e-09342
pituitary gland1.03e-082
pineal body2.12e-082
regional part of epithalamus2.12e-082
secretory circumventricular organ2.12e-082
circumventricular organ2.12e-082
epithalamus2.12e-082
corpus striatum3.23e-084
striatum3.23e-084
ventral part of telencephalon3.23e-084
future corpus striatum3.23e-084
middle frontal gyrus5.13e-082
locus ceruleus6.54e-082
brainstem nucleus6.54e-082
hindbrain nucleus6.54e-082
Ammon's horn7.78e-082
lobe parts of cerebral cortex7.78e-082
hippocampal formation7.78e-082
limbic lobe7.78e-082
middle temporal gyrus8.33e-082
small intestine9.06e-074


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)
MA0003.10.000253048
MA0004.12.26719
MA0006.10.336062
MA0007.10.0928194
MA0009.11.09683
MA0014.10.203044
MA0017.12.09799
MA0019.10.188957
MA0024.10.343215
MA0025.10.544326
MA0027.11.97447
MA0028.10.04151
MA0029.10.942823
MA0030.12.49242
MA0031.10.299024
MA0038.10.160193
MA0040.10.953232
MA0041.10.111817
MA0042.10.0954223
MA0043.10.429296
MA0046.10.419892
MA0048.10.0769542
MA0050.10.654418
MA0051.10.157595
MA0052.10.366488
MA0055.10.518234
MA0056.10
MA0057.10.143357
MA0058.14.9544
MA0059.15.70828
MA0060.10.0102756
MA0061.11.57813
MA0063.10
MA0066.10.160456
MA0067.10.711124
MA0068.10.276719
MA0069.10.416668
MA0070.10.407339
MA0071.10.137013
MA0072.10.403605
MA0073.11.92081e-06
MA0074.10.157134
MA0076.10.065346
MA0077.10.397221
MA0078.10.222673
MA0081.12.86487
MA0083.10.435361
MA0084.10.887042
MA0087.11.03711
MA0088.10.00722381
MA0089.10
MA0090.13.81062
MA0091.12.28235
MA0092.10.287838
MA0093.12.94822
MA0095.10
MA0098.10
MA0100.10.168841
MA0101.10.0383945
MA0103.10.0336762
MA0105.11.21636
MA0106.10.18641
MA0107.10.414244
MA0108.22.23312
MA0109.10
MA0111.10.0774258
MA0113.10.197248
MA0114.11.3501
MA0115.16.46876
MA0116.10.0880779
MA0117.10.460927
MA0119.10.0523174
MA0122.10.483183
MA0124.10.60338
MA0125.10.528543
MA0130.10
MA0131.10.23543
MA0132.10
MA0133.10
MA0135.10.454747
MA0136.10.164568
MA0139.10.091521
MA0140.10.135474
MA0141.10.80074
MA0142.10.275028
MA0143.10.197366
MA0144.10.362892
MA0145.10.00027973
MA0146.10.0626807
MA0147.16.77168
MA0148.10.115217
MA0149.10.129939
MA0062.20.00628534
MA0035.20.135068
MA0039.28.21537e-08
MA0138.21.18977
MA0002.20.124839
MA0137.20.0436553
MA0104.25.63477
MA0047.20.178535
MA0112.20.0250176
MA0065.20.00254951
MA0150.10.0689331
MA0151.10
MA0152.10.139287
MA0153.10.513757
MA0154.12.55267
MA0155.10.00697357
MA0156.10.0444235
MA0157.10.708688
MA0158.10
MA0159.10.708322
MA0160.10.781079
MA0161.10
MA0162.13.64416e-05
MA0163.10.00321392
MA0164.10.205602
MA0080.20.966
MA0018.21.04817
MA0099.20.139496
MA0079.23.01511e-05
MA0102.20.922526
MA0258.10.338434
MA0259.11.48432
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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