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Coexpression cluster:C3416: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,1.18351,0.820209,0.985163,1.94915,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,1.45286,0.855276,1.39264,0.469078,0.598234,0.777097,0.718382,0.63803,0.461452,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,2.51002,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.886337,1.45054,1.92922,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,1.66424,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,2.2314,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.853445,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,1.51317,0.744018,0.710709,1.56892,1.35169,1.19946,1.69998,1.11698,0.960047,0.524529,0.936473,0.265282
|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;0.758317,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;0.190716,MA0056.1;0,MA0057.1;0.886807,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;10.8187,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;0.0834661,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;2.37746,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;1.3784,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;0.531867,MA0145.1;0.273764,MA0146.1;1.70974,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.0526989,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,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;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;1.38935,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;0.776149,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.481578,MA0102.2;1.88331,MA0258.1;1.29138,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 21:21, 22 January 2013


Full id: C3416_Alveolar_Renal_Mesothelial_Retinal_mesothelioma_mesenchymal_Ciliary



Phase1 CAGE Peaks

Hg19::chr14:24641209..24641246,+p2@REC8
Hg19::chr14:24641247..24641304,+p1@REC8
Hg19::chr14:24641311..24641322,+p3@REC8


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
epithelial cell of nephron1.57e-1215
kidney cortical cell2.75e-1012
renal cortical epithelial cell2.75e-1012
kidney cell4.26e-1017
kidney epithelial cell4.26e-1017
kidney tubule cell3.88e-0910
nephron tubule epithelial cell3.88e-0910
neural cell9.26e-0725
Uber Anatomy
Ontology termp-valuen
neural plate2.37e-3182
presumptive neural plate2.37e-3182
neurectoderm2.28e-3086
pre-chordal neural plate2.75e-2661
central nervous system7.10e-2681
nervous system5.21e-2589
neural tube1.13e-2356
neural rod1.13e-2356
future spinal cord1.13e-2356
neural keel1.13e-2356
ecto-epithelium3.13e-23104
regional part of nervous system2.43e-2253
regional part of brain2.43e-2253
brain6.83e-2068
future brain6.83e-2068
ectoderm-derived structure6.27e-18171
ectoderm6.27e-18171
presumptive ectoderm6.27e-18171
structure with developmental contribution from neural crest1.29e-17132
regional part of forebrain2.57e-1641
forebrain2.57e-1641
anterior neural tube2.57e-1641
future forebrain2.57e-1641
organ part5.50e-16218
anatomical cluster2.66e-15373
organ system subdivision9.86e-15223
brain grey matter1.30e-1334
gray matter1.30e-1334
telencephalon1.40e-1334
adult organism2.35e-13114
multi-tissue structure3.23e-13342
cerebral hemisphere5.81e-1332
regional part of telencephalon6.48e-1332
excretory tube1.28e-1216
kidney epithelium1.28e-1216
nephron epithelium1.57e-1215
renal tubule1.57e-1215
nephron tubule1.57e-1215
nephron1.57e-1215
uriniferous tubule1.57e-1215
nephrogenic mesenchyme1.57e-1215
cell layer1.28e-11309
epithelium2.64e-11306
eye3.21e-1121
visual system3.21e-1121
camera-type eye3.83e-1120
simple eye3.83e-1120
immature eye3.83e-1120
ocular region3.83e-1120
eyeball of camera-type eye3.83e-1120
optic cup3.83e-1120
optic vesicle3.83e-1120
eye primordium3.83e-1120
cerebral cortex1.80e-1025
pallium1.80e-1025
tube2.45e-10192
cortex of kidney2.75e-1012
renal parenchyma2.75e-1012
parenchyma1.11e-0915
embryo2.50e-09592
face2.61e-0922
nephron tubule epithelium3.88e-0910
posterior neural tube1.14e-0815
chordal neural plate1.14e-0815
sense organ1.15e-0824
sensory system1.15e-0824
entire sense organ system1.15e-0824
regional part of cerebral cortex1.18e-0822
cortex1.28e-0815
developing anatomical structure3.23e-08581
pigment epithelium of eye4.20e-0811
neocortex5.74e-0820
cavitated compound organ7.35e-0831
segmental subdivision of nervous system7.57e-0813
segmental subdivision of hindbrain2.00e-0712
hindbrain2.00e-0712
presumptive hindbrain2.00e-0712
anterior segment of eyeball2.02e-0714
organ segment2.46e-0798
kidney2.59e-0726
kidney mesenchyme2.59e-0726
upper urinary tract2.59e-0726
kidney rudiment2.59e-0726
kidney field2.59e-0726
intraembryonic coelom4.00e-0712
mesonephros6.20e-079
pronephros6.20e-079
nephrogenic cord6.20e-079
pronephric mesoderm6.20e-079
rostral part of nephrogenic cord6.20e-079
presumptive pronephric mesoderm6.20e-079


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
MA0014.10.758317
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
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.110.8187
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
MA0076.10.734647
MA0077.11.28751
MA0078.12.37746
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
MA0116.11.3784
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
MA0144.10.531867
MA0145.10.273764
MA0146.11.70974
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.481578
MA0102.21.88331
MA0258.11.29138
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#467214.97544968400580.005768294540793880.0259491261865081
EBF1#187938.9064668465690.00141523283560980.00913620361714998
EGR1#195834.988179094810140.008056488137383440.0319709538939201
ELF1#199734.258097958807540.01295179875054610.0461002286724928
EP300#203336.77394172622320.003216880500103790.0167164783834382
JUND#372736.994663941871030.002921845042734990.0156409315437314
PAX5#507936.669565531177830.003370290999677260.0172594793427132
POU2F2#545239.106124057742520.001324165192682130.0088080051307897
RFX5#5993312.04791082719510.0005717246050312580.00483719588665421
RXRA#6256213.38307809275550.007196434429465730.0298202037525381
SP1#666735.69838137814090.005403962701712170.0245908439982623
YY1#752834.911170749853860.008441455341808260.0328569303236103



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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