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Coexpression cluster:C3250: Difference between revisions

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{{Coexpression_clusters
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,0.575162,0.452865,0.305559,0.69094,1.95727,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,1.46099,0.427404,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,1.87308,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,8.5051,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,1.68795,1.39614,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,1.44883,2.36218,0.794219,1.10778,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,1.96632,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,2.3415,1.29196,1.37083,0.481626,0.941179,1.78371,1.03563,1.51317,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,1.3017,0.936473,0.265282|tfbs_overrepresentation_jaspar=MA0003.1;3.8806,MA0004.1;0.826076,MA0006.1;1.5435,MA0007.1;1.88666,MA0009.1;1.3275,MA0014.1;1.80735,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;0.341392,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;1.70014,MA0060.1;1.23283,MA0061.1;0.456531,MA0063.1;0,MA0066.1;3.5636,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;2.78116,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;0.715722,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;5.26983,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;1.66081,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;6.20416,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;7.95144,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;1.2307,MA0047.2;0.973066,MA0112.2;1.34467,MA0065.2;1.39232,MA0150.1;0.744617,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;2.05956,MA0163.1;1.84145,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;11.5899,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3250_liver_Hepatocyte_Melanocyte_Monocytederived_placenta_Meningeal_Pericytes
|id=C3250
}}

Latest revision as of 12:22, 17 September 2013


Full id: C3250_liver_Hepatocyte_Melanocyte_Monocytederived_placenta_Meningeal_Pericytes



Phase1 CAGE Peaks

Hg19::chr12:125348399..125348419,-p1@SCARB1
Hg19::chr12:125348434..125348445,-p4@SCARB1
Hg19::chr12:125348448..125348472,-p2@SCARB1


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 cell5.05e-27253
embryonic cell2.88e-12250
lining cell3.04e-0958
barrier cell3.04e-0958
meso-epithelial cell4.32e-0845
endothelial cell5.62e-0836
endodermal cell7.57e-0758
Uber Anatomy
Ontology termp-valuen
anatomical cluster1.70e-18373
multi-tissue structure1.09e-14342
cell layer3.51e-14309
epithelium2.15e-13306
subdivision of digestive tract4.22e-12118
abdomen element1.40e-1154
abdominal segment element1.40e-1154
trunk region element3.79e-11101
digestive system4.33e-11145
digestive tract4.33e-11145
primitive gut4.33e-11145
endoderm-derived structure6.18e-11160
endoderm6.18e-11160
presumptive endoderm6.18e-11160
abdominal segment of trunk4.62e-1060
abdomen4.62e-1060
organ system subdivision5.07e-10223
organism subdivision5.31e-10264
foregut2.51e-0987
subdivision of trunk3.01e-09112
liver6.68e-0919
digestive gland6.68e-0919
liver bud6.68e-0919
primordium1.58e-08160
exocrine gland2.57e-0831
exocrine system2.57e-0831
epithelium of foregut-midgut junction2.71e-0825
anatomical boundary2.71e-0825
hepatobiliary system2.71e-0825
foregut-midgut junction2.71e-0825
septum transversum2.71e-0825
anatomical conduit4.76e-08240
organ segment6.04e-0898
hepatic diverticulum6.68e-0822
liver primordium6.68e-0822
organ part8.74e-08218
digestive tract diverticulum1.23e-0723
endo-epithelium3.31e-0782
trunk3.54e-07199
larynx3.64e-079
epithelial sac4.17e-0725
immaterial anatomical entity4.77e-07117
sac6.70e-0726
tube7.34e-07192
eye8.70e-0721
visual system8.70e-0721
unilaminar epithelium8.80e-07148
Disease
Ontology termp-valuen
cancer1.06e-09235
disease of cellular proliferation3.03e-09239
carcinoma5.29e-08106


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)
MA0003.13.8806
MA0004.10.826076
MA0006.11.5435
MA0007.11.88666
MA0009.11.3275
MA0014.11.80735
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.11.70014
MA0060.11.23283
MA0061.10.456531
MA0063.10
MA0066.13.5636
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.12.78116
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0106.15.26983
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.11.66081
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
MA0146.16.20416
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.27.95144
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.21.34467
MA0065.21.39232
MA0150.10.744617
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
MA0162.12.05956
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.211.5899
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#90536.336201576962630.003930750035764890.0189347171710368
CTCF#1066435.360256373075030.0064925092527670.0278571617373869
CTCFL#140690319.74647435897440.0001298372005551160.00171299486972913
E2F6#187635.017155731697390.00791769806886330.0320771352113741
EBF1#187938.9064668465690.00141523283560980.00912886802039728
EGR1#195834.988179094810140.008056488137383440.0319357636383721
ELF1#199734.258097958807540.01295179875054610.0460437371403187
GABPB1#255337.067683836182170.002832212825417420.0153698869978576
IRF1#365937.63716375356390.002244692747297240.0127728814337461
MAX#414936.452555509007120.003721913834265510.0185933683601289
MXI1#460139.96157162875930.001011470541259020.00718667745142874
MYC#460935.22228187160940.007020843755740150.0293429069192743
POU2F2#545239.106124057742520.001324165192682130.00880071837587686
RAD21#5885310.35503389545630.0009004912073565420.0066220533167941
SIN3A#2594235.408884726815140.006318961977991520.0275689727637838
SMC3#9126315.04493284493280.0002935825420371870.00308248387532138
SP1#666735.69838137814090.005403962701712170.0245651560654676
SPI1#668838.204323508522730.001810593189410520.0108851336696319
TCF12#6938310.63446490218640.0008313523990202070.00628033368544458
TFAP2A#7020316.5186343730450.0002218033880766340.00247567853450204
TFAP2C#7022310.80922860986020.0007916746575753130.00613593391929559
YY1#752834.911170749853860.008441455341808260.0328226788698106
ZBTB7A#5134137.35190930787590.002516255860282270.0139717819018565



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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