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Coexpression cluster:C1254: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.0462779,MA0004.1;0.502801,MA0006.1;0.341337,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.0156227,MA0017.1;0.991615,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;5.48069,MA0028.1;0.35747,MA0029.1;0.886702,MA0030.1;0.875089,MA0031.1;0.809638,MA0038.1;0.60704,MA0040.1;0.892629,MA0041.1;0.521615,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;0.120314,MA0050.1;1.22833,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;1.01052,MA0056.1;0,MA0057.1;0.369442,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;0.638423,MA0061.1;0.198335,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;1.51089,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;1.40685,MA0074.1;0.60198,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.0723293,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;0.467172,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.347695,MA0103.1;0.332048,MA0105.1;0.340955,MA0106.1;0.648997,MA0107.1;0.274127,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;0.741402,MA0115.1;1.21667,MA0116.1;0.277571,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;0.722072,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;0.614215,MA0139.1;0.186511,MA0140.1;0.564957,MA0141.1;1.04059,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;0.0807715,MA0146.1;0.162729,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;1.38583,MA0039.2;0.00276064,MA0138.2;0.704862,MA0002.2;0.611548,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;0.944394,MA0065.2;0.0828768,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.685508,MA0155.1;0.071478,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.106355,MA0163.1;0.0167306,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;0.07638,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:48, 22 January 2013


Full id: C1254_leiomyoblastoma_occipital_rhabdomyosarcoma_parietal_temporal_brain_medial



Phase1 CAGE Peaks

Hg19::chr1:190446762..190446774,-p4@FAM5C
Hg19::chr1:190446924..190446931,-p8@FAM5C
Hg19::chr1:190446947..190446956,-p5@FAM5C
Hg19::chr1:190446983..190447001,-p1@FAM5C
Hg19::chr1:190447030..190447044,-p3@FAM5C
Hg19::chr7:8473187..8473196,+p9@NXPH1
Hg19::chr7:8473232..8473245,+p1@NXPH1


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 tube5.23e-8356
neural rod5.23e-8356
future spinal cord5.23e-8356
neural keel5.23e-8356
regional part of nervous system1.78e-7553
regional part of brain1.78e-7553
central nervous system2.90e-7181
nervous system8.45e-6689
brain1.16e-6568
future brain1.16e-6568
brain grey matter1.54e-6334
gray matter1.54e-6334
telencephalon2.53e-6334
cerebral hemisphere6.73e-5932
regional part of forebrain9.93e-5941
forebrain9.93e-5941
anterior neural tube9.93e-5941
future forebrain9.93e-5941
regional part of telencephalon2.01e-5832
neural plate2.84e-5382
presumptive neural plate2.84e-5382
regional part of cerebral cortex6.53e-5322
neurectoderm2.80e-5086
neocortex7.94e-4820
cerebral cortex4.40e-4625
pallium4.40e-4625
ecto-epithelium9.72e-42104
structure with developmental contribution from neural crest2.50e-39132
adult organism7.64e-39114
pre-chordal neural plate7.10e-3761
ectoderm-derived structure4.60e-30171
ectoderm4.60e-30171
presumptive ectoderm4.60e-30171
organ system subdivision1.30e-29223
posterior neural tube2.93e-2415
chordal neural plate2.93e-2415
tube8.02e-22192
neural nucleus1.62e-189
nucleus of brain1.62e-189
basal ganglion1.69e-189
nuclear complex of neuraxis1.69e-189
aggregate regional part of brain1.69e-189
collection of basal ganglia1.69e-189
cerebral subcortex1.69e-189
segmental subdivision of hindbrain3.60e-1712
hindbrain3.60e-1712
presumptive hindbrain3.60e-1712
anatomical cluster3.75e-16373
brainstem3.91e-166
segmental subdivision of nervous system1.04e-1513
occipital lobe2.06e-155
parietal lobe2.76e-155
temporal lobe4.06e-156
anatomical conduit4.69e-15240
limbic system1.62e-145
telencephalic nucleus1.44e-137
gyrus1.61e-126
organ part3.66e-12218
corpus striatum7.92e-124
striatum7.92e-124
ventral part of telencephalon7.92e-124
future corpus striatum7.92e-124
multi-tissue structure1.66e-11342
regional part of metencephalon9.86e-119
metencephalon9.86e-119
future metencephalon9.86e-119
epithelium1.28e-10306
cell layer2.11e-10309
spinal cord3.07e-093
dorsal region element3.07e-093
dorsum3.07e-093
pons4.29e-093
caudate-putamen4.66e-093
dorsal striatum4.66e-093
medulla oblongata9.79e-093
myelencephalon9.79e-093
future myelencephalon9.79e-093
organ3.57e-08503
middle temporal gyrus3.46e-072
locus ceruleus9.32e-072
brainstem nucleus9.32e-072
hindbrain nucleus9.32e-072
amygdala9.86e-072


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)
MA0003.10.0462779
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
MA0017.10.991615
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.15.48069
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.11.22833
MA0051.10.602745
MA0052.10.896548
MA0055.11.01052
MA0056.10
MA0057.10.369442
MA0058.10.406232
MA0059.10.404929
MA0060.10.638423
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.11.51089
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.11.40685
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.340955
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.741402
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.11.04059
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.0807715
MA0146.10.162729
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.21.38583
MA0039.20.00276064
MA0138.20.704862
MA0002.20.611548
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.944394
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.685508
MA0155.10.071478
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.106355
MA0163.10.0167306
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.07638
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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
CTBP2#1488217.91914295409380.005060297063777310.023568157556361
SUZ12#23512428.63758909203595.27895839013948e-060.000161396116893377



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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