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Coexpression cluster:C4235: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;1.0927,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;6.45108,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.904546,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.557638,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.990225,MA0074.1;0.935474,MA0076.1;0.734647,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;2.5782,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;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;1.31729,MA0145.1;0.752137,MA0146.1;0.107247,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;4.75888,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;1.60005,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.277623,MA0150.1;1.76247,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;3.71118,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;5.63764,MA0164.1;1.01792,MA0080.2;1.55139,MA0018.2;0.987913,MA0099.2;2.08754,MA0079.2;8.812,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 21:55, 22 January 2013


Full id: C4235_nonsmall_endometrial_colon_small_tubular_argyrophil_Prostate



Phase1 CAGE Peaks

Hg19::chr2:47596330..47596380,+p2@EPCAM
Hg19::chr2:47596386..47596392,+p7@EPCAM
Hg19::chr2:47596394..47596400,+p6@EPCAM


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell9.42e-28253
endodermal cell2.08e-1458
endo-epithelial cell2.19e-1242
germ line cell3.93e-097
germ cell3.93e-097
kidney tubule cell4.96e-0910
nephron tubule epithelial cell4.96e-0910
epithelial cell of alimentary canal5.02e-0920
epithelial cell of lung2.84e-0719
Uber Anatomy
Ontology termp-valuen
digestive system8.26e-17145
digestive tract8.26e-17145
primitive gut8.26e-17145
endoderm-derived structure9.17e-16160
endoderm9.17e-16160
presumptive endoderm9.17e-16160
endo-epithelium2.16e-1482
trunk region element8.14e-14101
subdivision of digestive tract3.44e-13118
immaterial anatomical entity9.92e-11117
epithelial bud1.77e-0937
gastrointestinal system3.65e-0925
subdivision of trunk4.22e-09112
nephron tubule epithelium4.96e-0910
anatomical space5.06e-0995
intestine8.48e-0917
urinary system structure1.77e-0847
kidney1.84e-0826
kidney mesenchyme1.84e-0826
upper urinary tract1.84e-0826
kidney rudiment1.84e-0826
kidney field1.84e-0826
gut epithelium2.40e-0854
renal system3.76e-0848
cavitated compound organ3.83e-0831
lung4.45e-0822
respiratory tube4.45e-0822
respiration organ4.45e-0822
pair of lungs4.45e-0822
lung primordium4.45e-0822
lung bud4.45e-0822
abdomen element6.52e-0854
abdominal segment element6.52e-0854
respiratory tract epithelium2.84e-0719
lung epithelium2.84e-0719
mucosa2.97e-0720
excretory tube6.00e-0716
kidney epithelium6.00e-0716
respiratory system epithelium8.53e-0728
reproductive structure9.83e-0759
reproductive system9.83e-0759
Disease
Ontology termp-valuen
carcinoma3.37e-44106
cell type cancer1.41e-33143
cancer2.70e-18235
disease of cellular proliferation7.26e-18239
adenocarcinoma7.81e-1625
squamous cell carcinoma1.00e-1314
gastrointestinal system cancer1.20e-0714
respiratory system cancer6.29e-0716
disease of anatomical entity6.86e-0739


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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.16.45108
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
MA0055.10.557638
MA0056.10
MA0057.10.333427
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
MA0073.10.990225
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.12.5782
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.11.31729
MA0145.10.752137
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.24.75888
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.11.76247
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.13.71118
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.15.63764
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.22.08754
MA0079.28.812
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
ATF3#467322.46317452600878.81932387510763e-050.00129839493401799
CCNT2#90536.336201576962630.003930750035764890.0190515872927998
E2F1#186934.907389214879320.008460985347239390.0326361666671715
E2F6#187635.017155731697390.00791769806886330.0323190990625347
EP300#203336.77394172622320.003216880500103790.0167866384805806
FOS#235338.99795530889440.001372499272417130.00899601176804146
FOSL1#8061339.7135797163731.59554825631833e-050.000371792646902343
FOSL2#2355316.93020060456170.0002060162053171620.00243587982193129
JUN#3725312.51282919233630.0005103313992726250.00445118598702469
JUND#372736.994663941871030.002921845042734990.0157134178382183
MYC#460935.22228187160940.007020843755740150.029527237990003
NANOG#79923329.24477848101273.99627955670032e-050.000739357733608902
RXRA#6256320.07461713913330.0001235730348432220.00165544435428313
SP1#666735.69838137814090.005403962701712170.0247146812315693
TAF7#6879311.43306940492390.0006690181981945830.00544383261404317
TCF12#6938310.63446490218640.0008313523990202070.00630358742567674
YY1#752834.911170749853860.008441455341808260.0330206058070757
ZNF263#1012738.221841637010680.001799043925565870.0109678564323259



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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