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Coexpression cluster:C2968: Difference between revisions

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{{Coexpression_clusters
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234,0.777097,0.259059,0.63803,0.151453,1.72524,0.939121,0.808003,0.247669,1.55608,2.33699,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,2.20718,4.08293,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,3.91579,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,2.58159,0.960908,0.498519,1.39759,1.55552,0.82001,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,1.54991,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,2.12604,1.7605,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,1.05469,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,1.87432,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,1.33389,1.54007,1.29196,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,1.69223,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.56135|tfbs_overrepresentation_jaspar=MA0003.1;2.61626,MA0004.1;3.20493,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;3.14798,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;0.714521,MA0060.1;1.23283,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;1.04561,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.407479,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;2.626,MA0095.1;0,MA0098.1;0,MA0100.1;3.60951,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;2.29491,MA0114.1;0.549955,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;0.531867,MA0145.1;0.273764,MA0146.1;0.107247,MA0147.1;3.48176,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;1.62945,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;3.15214,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;1.51687,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;5.21222,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.941469,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;2.40872,MA0442.1;0}}
|full_id=C2968_CD14_acute_medulloblastoma_liver_Fibroblast_myelodysplastic_granulocyte
|id=C2968
}}

Latest revision as of 12:16, 17 September 2013


Full id: C2968_CD14_acute_medulloblastoma_liver_Fibroblast_myelodysplastic_granulocyte



Phase1 CAGE Peaks

Hg19::chr10:101945654..101945676,-p5@ERLIN1
Hg19::chr10:101945681..101945710,-p3@ERLIN1
Hg19::chr10:101945716..101945735,-p2@ERLIN1


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
animal cell1.17e-17679
eukaryotic cell1.17e-17679
somatic cell1.21e-10588
embryonic cell1.27e-08250
non-terminally differentiated cell2.00e-07106
fibroblast2.92e-0776
skin fibroblast4.20e-0723
stem cell5.06e-07441
Uber Anatomy
Ontology termp-valuen
unilaminar epithelium7.08e-08148
Disease
Ontology termp-valuen
myeloid leukemia2.11e-0831


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)
MA0003.12.61626
MA0004.13.20493
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.13.14798
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
MA0059.10.714521
MA0060.11.23283
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.407479
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
MA0093.12.626
MA0095.10
MA0098.10
MA0100.13.60951
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.12.29491
MA0114.10.549955
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
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.13.48176
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.23.15214
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.15.21222
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.941469
MA0102.21.88331
MA0258.10.519674
MA0259.12.40872
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
BCLAF1#9774321.65264761012189.8473954032885e-050.00138773732090682
BHLHE40#8553344.87181354697741.10603738662898e-050.000283538140947825
BRCA1#672320.18423064322380.0001215704860271640.00163870676176961
CCNT2#90536.336201576962630.003930750035764890.0188981081335566
CHD2#1106310.34402283411690.0009033701102746880.00658067035969716
E2F1#186934.907389214879320.008460985347239390.0323245728748705
E2F4#1874312.66806031528440.0004917987006298980.00434984455412313
E2F6#187635.017155731697390.00791769806886330.0320150400175777
EGR1#195834.988179094810140.008056488137383440.031881311176879
ELF1#199734.258097958807540.01295179875054610.0459655059707858
ELK4#2005316.2356816584680.0002336043955745990.00255016300506068
EP300#203336.77394172622320.003216880500103790.0166725116644504
FOS#235338.99795530889440.001372499272417130.00894325252757503
FOSL2#2355316.93020060456170.0002060162053171620.00242216891445672
FOXA1#3169311.08141974938550.000734755275698670.00579104265630468
HDAC2#3066313.41562023662630.0004140761399857210.00389706208740819
HMGN3#932438.178547723350590.001827766942164210.0108245053401014
JUN#3725312.51282919233630.0005103313992726250.00442899293739685
JUND#372736.994663941871030.002921845042734990.0156081312678737
MAX#414936.452555509007120.003721913834265510.0185596332571073
MXI1#460139.96157162875930.001011470541259020.00717935108458278
MYC#460935.22228187160940.007020843755740150.0292971831950514
NANOG#79923329.24477848101273.99627955670032e-050.000733897381083568
NFKB1#479035.488063424193840.006049381815655430.0268379162926485
NRF1#4899312.21027944771090.0005492172401020010.0046912324641378
PAX5#507936.669565531177830.003370290999677260.0172164256158128
REST#597839.650028716128020.001112636247114590.00764994187046746
SIN3A#2594235.408884726815140.006318961977991520.0275218345226847
TCF7L2#6934310.77017656313730.0008003181298398380.00611310064816374
TFAP2A#7020316.5186343730450.0002218033880766340.00247224376172205
TFAP2C#7022310.80922860986020.0007916746575753130.00612547855700905
USF1#739136.361499277207960.00388404057290560.0189368056296946
WRNIP1#568973109.8199643493767.53682839543883e-073.31986006238395e-05
YY1#752834.911170749853860.008441455341808260.0327689991987479
ZNF263#1012738.221841637010680.001799043925565870.0108852527977623



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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