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Coexpression cluster:C1274: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.79738,1.1011,0.384703,0.529489,0.343148,1.30874,1.47005,0.226729,0.224331,0.0544999,0.497563,0.647852,0.184039,0.592674,1.62257,0.365029,0.827563,0.28906,0.19568,0.0986842,0.384762,0.85713,2.22719,0.338096,0.430372,0.670692,0.957451,0.517892,0.346214,2.77567,0.475674,0.864517,0.257226,1.04347,2.29455,0.021349,0.305874,0.529001,0.282922,0.207499,0.307642,0.459366,0.541549,1.61728,0.0257952,0.415364,0.60533,1.22101,0.237549,1.63856,0.684981,0.617179,0.373994,0.941629,1.09491,0.595623,0.350547,0.562713,0.150585,2.36353,0.905643,2.51267,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,3.07478,0.4462,0.232216,0.115253,1.0929,0.179863,0.168304,0.921933,0.782748,0.850825,0.424224,0.200147,0.798651,0.625403,0.229431,1.04131,0.896187,0.097572,0.448771,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,1.07593,0.924148,0.715799,1.92468,2.17049,0.875714,0.918549,0.831244,0.753567,2.13786,0.815341,0.589207,0.43012,2.38505,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,0.039977,2.07616,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,1.45665,0.886402,1.12733,0.76179,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,3.49907,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,0.703388,1.33628,1.0153,0.216774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,6.22113,0.404861,0.7715,0.624608,0.24928,0.602897,4.41087
|tfbs_overrepresentation_for_novel_motifs=1.79738,1.1011,0.384703,0.529489,0.343148,1.30874,1.47005,0.226729,0.224331,0.0544999,0.497563,0.647852,0.184039,0.592674,1.62257,0.365029,0.827563,0.28906,0.19568,0.0986842,0.384762,0.85713,2.22719,0.338096,0.430372,0.670692,0.957451,0.517892,0.346214,2.77567,0.475674,0.864517,0.257226,1.04347,2.29455,0.021349,0.305874,0.529001,0.282922,0.207499,0.307642,0.459366,0.541549,1.61728,0.0257952,0.415364,0.60533,1.22101,0.237549,1.63856,0.684981,0.617179,0.373994,0.941629,1.09491,0.595623,0.350547,0.562713,0.150585,2.36353,0.905643,2.51267,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,3.07478,0.4462,0.232216,0.115253,1.0929,0.179863,0.168304,0.921933,0.782748,0.850825,0.424224,0.200147,0.798651,0.625403,0.229431,1.04131,0.896187,0.097572,0.448771,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,1.07593,0.924148,0.715799,1.92468,2.17049,0.875714,0.918549,0.831244,0.753567,2.13786,0.815341,0.589207,0.43012,2.38505,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,0.039977,2.07616,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,1.45665,0.886402,1.12733,0.76179,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,3.49907,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,0.703388,1.33628,1.0153,0.216774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,6.22113,0.404861,0.7715,0.624608,0.24928,0.602897,4.41087
|tfbs_overrepresentation_jaspar=MA0003.1;0.00215847,MA0004.1;0.502801,MA0006.1;0.341337,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;4.31657,MA0017.1;0.380797,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;0.35747,MA0029.1;0.886702,MA0030.1;0.875089,MA0031.1;0.809638,MA0038.1;0.60704,MA0040.1;0.892629,MA0041.1;0.521615,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;0.120314,MA0050.1;3.14713,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;0.0407081,MA0056.1;0,MA0057.1;0.115382,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;4.34287,MA0061.1;0.198335,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;0.162298,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.000265001,MA0074.1;0.60198,MA0076.1;1.08222,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;1.04478,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.0723293,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;0.467172,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.918548,MA0103.1;0.88373,MA0105.1;0.104569,MA0106.1;0.648997,MA0107.1;0.274127,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;0.269076,MA0115.1;1.21667,MA0116.1;1.39213,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;4.02117,MA0130.1;0,MA0131.1;1.71579,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;0.614215,MA0139.1;0.186511,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;3.05228,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;0.980834,MA0146.1;0.828373,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;1.07166,MA0035.2;0.564239,MA0039.2;0.0170091,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;2.55032,MA0065.2;0.0828768,MA0150.1;0.430951,MA0151.1;0,MA0152.1;2.39586,MA0153.1;1.07307,MA0154.1;0.102476,MA0155.1;0.071478,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;2.99895,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.0249953,MA0163.1;0.0167306,MA0164.1;1.62495,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;0.07638,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:49, 22 January 2013


Full id: C1274_Preadipocyte_Olfactory_Adipocyte_amniotic_serous_spindle_mesodermal



Phase1 CAGE Peaks

Hg19::chr5:125759038..125759049,+p7@GRAMD3
Hg19::chr5:125759064..125759131,+p1@GRAMD3
Hg19::chr5:125759140..125759175,+p2@GRAMD3
Hg19::chr5:125759213..125759224,+p5@GRAMD3
Hg19::chr5:125759230..125759241,+p6@GRAMD3
Hg19::chr5:125759251..125759262,+p13@GRAMD3
Hg19::chr5:125759280..125759291,+p12@GRAMD3


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
fibroblast1.79e-0776
Uber Anatomy
Ontology termp-valuen
adult organism2.60e-20114
neural tube3.37e-1956
neural rod3.37e-1956
future spinal cord3.37e-1956
neural keel3.37e-1956
regional part of nervous system2.58e-1753
regional part of brain2.58e-1753
ectoderm-derived structure8.75e-17171
ectoderm8.75e-17171
presumptive ectoderm8.75e-17171
ecto-epithelium1.01e-15104
brain6.92e-1568
future brain6.92e-1568
regional part of forebrain2.63e-1441
forebrain2.63e-1441
anterior neural tube2.63e-1441
future forebrain2.63e-1441
central nervous system1.41e-1381
structure with developmental contribution from neural crest4.98e-13132
neural plate1.88e-1282
presumptive neural plate1.88e-1282
nervous system1.47e-1189
telencephalon3.57e-1134
brain grey matter4.97e-1134
gray matter4.97e-1134
neurectoderm7.14e-1186
organ part2.08e-10218
regional part of telencephalon4.21e-1032
cerebral hemisphere4.25e-1032
organ component layer1.07e-0966
organ1.24e-09503
surface structure7.34e-0999
pre-chordal neural plate7.43e-0961
multi-cellular organism2.20e-08656
regional part of cerebral cortex5.91e-0822
organ system subdivision8.03e-08223
multi-tissue structure1.51e-07342
extraembryonic membrane1.60e-0714
membranous layer1.60e-0714
anatomical system1.86e-07624
anatomical group2.51e-07625
neocortex7.76e-0720


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)
MA0003.10.00215847
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.14.31657
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.13.14713
MA0051.10.602745
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.14.34287
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.000265001
MA0074.10.60198
MA0076.11.08222
MA0077.10.934645
MA0078.10.703614
MA0081.11.04478
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.918548
MA0103.10.88373
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.11.39213
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.14.02117
MA0130.10
MA0131.11.71579
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.13.05228
MA0143.10.66587
MA0144.10.254954
MA0145.10.980834
MA0146.10.828373
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.21.07166
MA0035.20.564239
MA0039.20.0170091
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.22.55032
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.12.39586
MA0153.11.07307
MA0154.10.102476
MA0155.10.071478
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.12.99895
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.0167306
MA0164.11.62495
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.07638
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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
E2F1#186974.907389214879321.45832274679793e-050.000346937971190954
ELK4#2005716.2356816584683.35702334142222e-092.76938515604103e-07
GABPB1#255344.038676477818380.00980113494696150.0368513782167157
HDAC2#3066713.41562023662631.27676792256388e-089.45034479551018e-07
MYC#460975.22228187160949.4355989882785e-060.000251068668213202
NFKB1#479075.488063424193846.66568321176054e-060.000194947434599008
PBX3#5090721.91451268674414.11002992557057e-104.03428021989347e-08
POLR2A#543072.147453176558070.004747636447610280.022356210963162
RFX5#5993712.04791082719512.7106444306642e-081.86125571133556e-06
SMARCB1#6598615.64518495527781.8015574550748e-079.86126095652814e-06
SP1#666775.69838137814095.12280185510121e-060.000157312644206091
TAF1#687273.343046285745290.0002142336319622450.002468212497353
TBP#690873.706770687096390.0001039672097505110.00145221765669836
TCF12#6938710.63446490218646.49404108872792e-083.973234664708e-06
ZNF263#1012778.221841637010683.93423095812578e-071.90932689142982e-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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