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Coexpression cluster:C3517: Difference between revisions

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{{Coexpression_clusters
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033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.0834661,MA0074.1;0.935474,MA0076.1;2.91768,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;1.35563,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;2.91906,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;1.31729,MA0145.1;0.273764,MA0146.1;0.348055,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;1.9924,MA0035.2;0.894194,MA0039.2;0.757898,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;4.7367,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;2.02721,MA0156.1;1.60572,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;9.44515,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;4.62164,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3517_Wilms_small_left_Dendritic_brain_adrenal_Placental
|id=C3517
}}

Latest revision as of 12:27, 17 September 2013


Full id: C3517_Wilms_small_left_Dendritic_brain_adrenal_Placental



Phase1 CAGE Peaks

Hg19::chr15:78423705..78423738,-p2@CIB2
Hg19::chr15:78423763..78423774,-p3@CIB2
Hg19::chr15:78423776..78423794,-p1@CIB2


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
ectodermal cell3.11e-0772
Uber Anatomy
Ontology termp-valuen
anatomical cluster9.07e-20373
ecto-epithelium3.59e-19104
neural plate6.18e-1982
presumptive neural plate6.18e-1982
ectoderm-derived structure2.61e-18171
ectoderm2.61e-18171
presumptive ectoderm2.61e-18171
central nervous system3.15e-1781
neurectoderm6.47e-1786
nervous system5.49e-1589
organ part1.04e-14218
multi-tissue structure5.97e-14342
cell layer6.12e-14309
epithelium9.46e-14306
neural tube1.59e-1356
neural rod1.59e-1356
future spinal cord1.59e-1356
neural keel1.59e-1356
pre-chordal neural plate2.85e-1361
brain1.14e-1268
future brain1.14e-1268
regional part of nervous system1.21e-1253
regional part of brain1.21e-1253
adult organism1.61e-12114
organ system subdivision2.02e-12223
structure with developmental contribution from neural crest2.15e-11132
renal system3.41e-1148
urinary system structure5.47e-1147
tube3.84e-10192
cavitated compound organ1.11e-0931
anatomical conduit1.97e-09240
regional part of forebrain7.81e-0941
forebrain7.81e-0941
anterior neural tube7.81e-0941
future forebrain7.81e-0941
compound organ1.19e-0868
kidney2.33e-0826
kidney mesenchyme2.33e-0826
upper urinary tract2.33e-0826
kidney rudiment2.33e-0826
kidney field2.33e-0826
brain grey matter3.57e-0834
gray matter3.57e-0834
cerebral hemisphere3.69e-0832
embryo6.73e-08592
telencephalon9.64e-0834
cerebral cortex1.06e-0725
pallium1.06e-0725
regional part of telencephalon1.42e-0732
multi-cellular organism2.89e-07656
anatomical system9.05e-07624
trunk region element9.61e-07101


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)
MA0003.13.22681
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.14.7105
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.12.67616
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
MA0055.10.190716
MA0056.10
MA0057.10.886807
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
MA0073.10.0834661
MA0074.10.935474
MA0076.12.91768
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
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
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
MA0144.11.31729
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.24.7367
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.12.02721
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.19.44515
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.24.62164
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#90536.336201576962630.003930750035764890.0189688385077742
CTCF#1066435.360256373075030.0064925092527670.0279018670829452
CTCFL#140690319.74647435897440.0001298372005551160.00171494465521384
E2F4#1874312.66806031528440.0004917987006298980.00436462988571431
E2F6#187635.017155731697390.00791769806886330.0321469684179145
EGR1#195834.988179094810140.008056488137383440.0319904024249179
ELF1#199734.258097958807540.01295179875054610.0461269534427377
ELK4#2005316.2356816584680.0002336043955745990.00255497009837842
ETS1#211339.728760922202340.001085840092584840.00761101029727971
GABPB1#255337.067683836182170.002832212825417420.0153882777688987
HMGN3#932438.178547723350590.001827766942164210.0108559003453531
PAX5#507936.669565531177830.003370290999677260.0172662524141712
RAD21#5885310.35503389545630.0009004912073565420.00663139199020659
SMC3#9126315.04493284493280.0002935825420371870.00308589644804969
YY1#752834.911170749853860.008441455341808260.0328691803162744
ZBTB7A#5134137.35190930787590.002516255860282270.013989632461646
ZEB1#6935316.88843201754390.0002075486917327580.00242435721014176
ZNF143#7702313.50087655222790.0004062804962997170.00388460393234881



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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