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Coexpression cluster:C4036: Difference between revisions

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{{Coexpression_clusters
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27,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.00417402,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=1.66899,0.869629,0.690871,0.855819,0.641468,0.853988,2.1595,0.494933,0.491742,1.18351,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,1.46099,0.137917,0.596053,1.99037,0.567465,1.18324,0.598234,0.777097,0.718382,0.63803,0.461452,2.89234,0.939121,1.89324,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,2.14035,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.886337,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,1.55552,2.26789,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,3.17067,4.24457,0.921547,1.7605,0.622396,0.703975,1.26794,0.684398,1.94007,1.58942,0.594137,1.66424,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,1.73097,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,1.33389,4.20421,1.29196,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,2.24188,0.936473,3.92523|tfbs_overrepresentation_jaspar=MA0003.1;0.401049,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;4.7105,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;1.62115,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;1.15625,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;2.0778,MA0072.1;1.29561,MA0073.1;0.0185922,MA0074.1;0.935474,MA0076.1;1.74184,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;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;0.549955,MA0115.1;1.57693,MA0116.1;2.36034,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;2.07172,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;3.85295,MA0146.1;6.20416,MA0147.1;1.38767,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;2.07011,MA0039.2;1.15986,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;2.94916,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.711948,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;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;2.26143,MA0099.2;0.902716,MA0079.2;1.22771,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4036_salivary_CD19_lung_alveolar_bronchogenic_Eosinophils_renal
|id=C4036
|ontology_enrichment_celltype=CL:0000236!3.93e-07!14;CL:0000738!3.97e-07!140
|ontology_enrichment_disease=DOID:0050687!1.82e-15!143;DOID:305!2.22e-15!106;DOID:14566!1.33e-08!239;DOID:1749!1.49e-08!14;DOID:162!2.19e-08!235
|ontology_enrichment_uberon=UBERON:0001007!8.84e-07!155;UBERON:0001555!8.84e-07!155;UBERON:0007026!8.84e-07!155
}}

Latest revision as of 12:38, 17 September 2013


Full id: C4036_salivary_CD19_lung_alveolar_bronchogenic_Eosinophils_renal



Phase1 CAGE Peaks

Hg19::chr20:42839224..42839236,-p@chr20:42839224..42839236
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Hg19::chr20:42839248..42839266,-p@chr20:42839248..42839266
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Hg19::chr20:42839289..42839310,-p@chr20:42839289..42839310
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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><br><br>disease_data<br>

Disease
Ontology termp-valuen
cell type cancer1.36e-15143
carcinoma4.09e-15106
disease of cellular proliferation7.80e-10239
cancer1.55e-09235
squamous cell carcinoma3.36e-0814


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.14.7105
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
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.12.0778
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.11.74184
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
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.12.36034
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
MA0140.12.07172
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.13.85295
MA0146.16.20416
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.22.07011
MA0039.21.15986
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.12.94916
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.22.26143
MA0099.20.902716
MA0079.21.22771
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-050.00129711500660803
BHLHE40#8553344.87181354697741.10603738662898e-050.000284796446307061
BRCA1#672320.18423064322380.0001215704860271640.001642947721298
CCNT2#90536.336201576962630.003930750035764890.0190295092469869
CEBPB#105137.971147625824820.001974187055288560.0115353094924069
CHD2#1106310.34402283411690.0009033701102746880.00661064118182302
E2F1#186934.907389214879320.008460985347239390.0325844186245929
E2F4#1874312.66806031528440.0004917987006298980.00437727667420197
E2F6#187635.017155731697390.00791769806886330.0322787285742062
ELF1#199734.258097958807540.01295179875054610.0462974607149359
EP300#203336.77394172622320.003216880500103790.0167673694939532
ETS1#211339.728760922202340.001085840092584840.00763252479670667
FOS#235338.99795530889440.001372499272417130.00898642414343756
FOXA1#3169311.08141974938550.000734755275698670.00582047225718244
GABPB1#255337.067683836182170.002832212825417420.0154316295530974
HDAC2#3066313.41562023662630.0004140761399857210.00391682800325774
HMGN3#932438.178547723350590.001827766942164210.0108837534450475
HNF4G#3174328.75342252644684.20470658818262e-050.000757391085483278
IRF1#365937.63716375356390.002244692747297240.0128266928836777
JUN#3725312.51282919233630.0005103313992726250.00444784286143985
JUND#372736.994663941871030.002921845042734990.0156996745597674
MAFK#7975327.10073313782995.02195559325033e-050.000858268728855296
MAX#414936.452555509007120.003721913834265510.0186827337756827
MXI1#460139.96157162875930.001011470541259020.00720923850805644
MYC#460935.22228187160940.007020843755740150.0294904239464988
NFKB1#479035.488063424193840.006049381815655430.0269915575445481
NR2C2#7182332.61461090524092.88098172333076e-050.000605284349633759
NRF1#4899312.21027944771090.0005492172401020010.00471630482971657
RFX5#5993312.04791082719510.0005717246050312580.00485213278277747
SIN3A#2594235.408884726815140.006318961977991520.0277206733321904
SMARCB1#6598318.25271578115740.000164397760679890.00203286025664777
SMARCC2#6601394.15537442689761.19621075407887e-064.85735050331426e-05
SP1#666735.69838137814090.005403962701712170.024690894242896
STAT3#6774310.51946499715420.0008589184530415310.0064336645138926
TAF7#6879311.43306940492390.0006690181981945830.00543874769216502
TCF12#6938310.63446490218640.0008313523990202070.00629901430653449
TFAP2A#7020316.5186343730450.0002218033880766340.00248470707361746
TFAP2C#7022310.80922860986020.0007916746575753130.00616475615586848
USF1#739136.361499277207960.00388404057290560.0190586973028419
USF2#7392312.99219738506960.0004558979393427810.00422105717083517
ZBTB7A#5134137.35190930787590.002516255860282270.0140412078324439
ZNF263#1012738.221841637010680.001799043925565870.0109576222395856



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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