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Coexpression cluster:C927: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.83884,1.39875,1.49249,0.440628,0.737182,0.439064,2.20019,0.164003,0.487494,0.840518,0.410439,0.553754,1.30067,2.16363,0.266007,0.287179,0.728104,0.218596,0.137566,0.473089,0.305279,0.0355541,0.431698,0.262652,1.64256,3.52871,0.112018,0.429643,0.74357,2.24764,0.389837,0.764231,5.82638,0.129565,0.23642,4.8191,0.659326,1.12093,0.213144,0.14756,0.235191,0.374544,0.0412835,0.264644,2.33975,1.59345,0.51292,0.4002,0.147122,0.270138,0.589559,0.524278,0.929597,0.839846,0.99088,0.503626,0.273964,0.472204,1.12004,2.06537,0.804523,0.5152,0.162346,0.700946,1.31866,0.667267,1.07848,1.44489,0.754027,1.28328,0.950736,0.168734,1.907,0.988898,1.27856,3.10091,0.105027,0.684401,0.750836,2.45513,0.141333,0.699894,0.532172,0.166331,0.937974,3.67076,25.042,1.61674,1.4924,1.54397,1.17124,0.911274,0.78075,0.196636,0.267904,0.207949,0.423564,0.82268,0.619373,0.0858425,1.15426,1.82563,0.817185,0.731699,0.656016,0.406162,0.716172,0.49749,0.347247,0.252953,0.315525,0.814459,0.300169,0.41935,1.12352,0.232218,1.01271,1.00897,0.664981,0.577715,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,0.50576,0.785662,1.02292,1.13275,0.911957,1.79896,7.19618,0.539846,1.18405,0.307751,0.384215,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,1.58202,0.464114,0.641461,1.83907,0.37143,1.07409,0.0656964,2.39813,0.912334,0.155464,1.28086,1.31376,0.599133,0.254737,0.347536,0.320853,1.10357,0.894035,0.750062,1.55897,0.673453,0.531409,1.63366,1.27204,0.0121205
|tfbs_overrepresentation_jaspar=MA0003.1;0.169975,MA0004.1;2.8046,MA0006.1;2.89341,MA0007.1;0.397529,MA0009.1;0.870971,MA0014.1;1.89045,MA0017.1;0.301634,MA0019.1;0.558663,MA0024.1;0.766783,MA0025.1;1.00397,MA0027.1;2.48103,MA0028.1;0.280275,MA0029.1;0.785955,MA0030.1;0.774581,MA0031.1;0.710608,MA0038.1;0.514558,MA0040.1;0.791764,MA0041.1;0.433167,MA0042.1;0.402577,MA0043.1;0.871285,MA0046.1;0.860127,MA0048.1;1.41801,MA0050.1;0.403421,MA0051.1;0.510444,MA0052.1;0.795605,MA0055.1;10.6619,MA0056.1;0,MA0057.1;0.253359,MA0058.1;0.325084,MA0059.1;0.323879,MA0060.1;0.162248,MA0061.1;0.432181,MA0063.1;0,MA0066.1;0.514973,MA0067.1;1.18766,MA0068.1;0.109867,MA0069.1;0.856287,MA0070.1;0.845142,MA0071.1;0.47692,MA0072.1;0.840664,MA0073.1;3.8275,MA0074.1;0.509711,MA0076.1;0.339975,MA0077.1;0.832987,MA0078.1;0.607575,MA0081.1;0.324031,MA0083.1;0.878452,MA0084.1;1.37471,MA0087.1;0.838229,MA0088.1;0.0408613,MA0089.1;0,MA0090.1;0.931587,MA0091.1;0.417885,MA0092.1;0.381858,MA0093.1;2.08959,MA0095.1;0,MA0098.1;0,MA0100.1;1.30927,MA0101.1;0.271368,MA0103.1;0.257174,MA0105.1;0.854766,MA0106.1;0.554855,MA0107.1;0.205358,MA0108.2;0.707575,MA0109.1;0,MA0111.1;0.366362,MA0113.1;1.39997,MA0114.1;0.200901,MA0115.1;1.11137,MA0116.1;2.50231,MA0117.1;0.908433,MA0119.1;2.29407,MA0122.1;0.934245,MA0124.1;1.06995,MA0125.1;0.986127,MA0130.1;0,MA0131.1;0.625452,MA0132.1;0,MA0133.1;0,MA0135.1;0.90122,MA0136.1;0.521435,MA0139.1;0.406919,MA0140.1;0.474342,MA0141.1;0.322254,MA0142.1;0.679161,MA0143.1;0.571113,MA0144.1;0.1885,MA0145.1;0.177438,MA0146.1;0.0260584,MA0147.1;0.607251,MA0148.1;0.439278,MA0149.1;0.464973,MA0062.2;0.135498,MA0035.2;0.473658,MA0039.2;0.00489248,MA0138.2;0.608783,MA0002.2;0.905786,MA0137.2;0.28622,MA0104.2;0.486672,MA0047.2;0.542971,MA0112.2;1.04513,MA0065.2;0.182082,MA0150.1;0.34802,MA0151.1;0,MA0152.1;0.480711,MA0153.1;0.969315,MA0154.1;0.062786,MA0155.1;0.156896,MA0156.1;0.288314,MA0157.1;0.652111,MA0158.1;0,MA0159.1;0.212043,MA0160.1;0.453945,MA0161.1;0,MA0162.1;0.767014,MA0163.1;0.101664,MA0164.1;0.583138,MA0080.2;0.268439,MA0018.2;0.556211,MA0099.2;0.481058,MA0079.2;0.000337902,MA0102.2;1.41188,MA0258.1;0.180288,MA0259.1;0.624802,MA0442.1;0
}}
}}

Revision as of 19:33, 22 January 2013


Full id: C927_Lens_gall_Ciliary_mesodermal_Fibroblast_Meningeal_cholangiocellular



Phase1 CAGE Peaks

Hg19::chr1:12416343..12416350,+p@chr1:12416343..12416350
+
Hg19::chr1:218519119..218519130,+p16@TGFB2
Hg19::chr1:218519150..218519159,+p20@TGFB2
Hg19::chr1:218519166..218519227,+p4@TGFB2
Hg19::chr1:218519393..218519489,+p2@TGFB2
Hg19::chr1:218519541..218519558,+p14@TGFB2
Hg19::chr1:218519582..218519594,+p8@TGFB2
Hg19::chr1:218519607..218519630,+p5@TGFB2
Hg19::chr1:218519642..218519668,+p3@TGFB2


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
non-terminally differentiated cell6.66e-07106
Uber Anatomy
Ontology termp-valuen
anatomical cluster9.39e-22373
multi-tissue structure3.26e-18342
cell layer4.08e-18309
structure with developmental contribution from neural crest7.90e-18132
epithelium7.13e-17306
anatomical conduit9.10e-17240
tube6.37e-15192
neural plate2.93e-1482
presumptive neural plate2.93e-1482
central nervous system6.88e-1481
brain2.02e-1368
future brain2.02e-1368
nervous system7.70e-1389
neurectoderm1.19e-1286
ecto-epithelium4.99e-12104
ectoderm-derived structure6.39e-12171
ectoderm6.39e-12171
presumptive ectoderm6.39e-12171
neural tube2.21e-1156
neural rod2.21e-1156
future spinal cord2.21e-1156
neural keel2.21e-1156
pre-chordal neural plate3.66e-1061
regional part of nervous system4.69e-1053
regional part of brain4.69e-1053
organ system subdivision6.59e-10223
brain grey matter7.12e-0934
gray matter7.12e-0934
vasculature of organ1.00e-0811
telencephalon1.36e-0834
regional part of telencephalon3.34e-0832
cerebral hemisphere4.79e-0832
regional part of forebrain5.19e-0841
forebrain5.19e-0841
anterior neural tube5.19e-0841
future forebrain5.19e-0841
embryonic structure1.21e-07564
anatomical system2.13e-07624
embryo2.20e-07592
vasculature2.51e-0778
vascular system2.51e-0778
anatomical group2.77e-07625
multi-cellular organism2.93e-07656
germ layer4.49e-07560
germ layer / neural crest4.49e-07560
embryonic tissue4.49e-07560
presumptive structure4.49e-07560
germ layer / neural crest derived structure4.49e-07560
epiblast (generic)4.49e-07560
cerebral cortex6.37e-0725
pallium6.37e-0725
developing anatomical structure8.52e-07581


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)
MA0003.10.169975
MA0004.12.8046
MA0006.12.89341
MA0007.10.397529
MA0009.10.870971
MA0014.11.89045
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.11.41801
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.110.6619
MA0056.10
MA0057.10.253359
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.10.432181
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.13.8275
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.0408613
MA0089.10
MA0090.10.931587
MA0091.10.417885
MA0092.10.381858
MA0093.12.08959
MA0095.10
MA0098.10
MA0100.11.30927
MA0101.10.271368
MA0103.10.257174
MA0105.10.854766
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.11.39997
MA0114.10.200901
MA0115.11.11137
MA0116.12.50231
MA0117.10.908433
MA0119.12.29407
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.406919
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.177438
MA0146.10.0260584
MA0147.10.607251
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.20.00489248
MA0138.20.608783
MA0002.20.905786
MA0137.20.28622
MA0104.20.486672
MA0047.20.542971
MA0112.21.04513
MA0065.20.182082
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.062786
MA0155.10.156896
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.767014
MA0163.10.101664
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.20.000337902
MA0102.21.41188
MA0258.10.180288
MA0259.10.624802
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#1488320.9056667797760.0003165442367723940.00324240521226678
CTCF#1066484.764672331622251.10088565904027e-050.000284874621765378
E2F1#186984.36212374655942.18983367577486e-050.000481178285849465
E2F6#187673.902232235764630.0003067423599492730.00316309886756933
POLR2A#543081.908847268051620.0116612289598830.0425864428051338
SMARCB1#6598816.22463624991776.9314124393577e-106.59899529402077e-08
ZNF263#1012787.308303677342823.84008362723504e-071.87496257103693e-05



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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