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Coexpression cluster:C1108: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.01633,1.1011,1.00019,0.529489,0.343148,0.52784,0.604235,0.226729,0.224331,0.443077,2.1529,0.647852,0.184039,0.592674,0.341795,0.365029,0.827563,0.28906,3.19478,0.0986842,0.384762,0.498384,3.28171,0.338096,1.09974,0.670692,0.957451,0.517892,0.346214,0.150685,0.475674,0.864517,0.257226,0.186138,0.309012,0.021349,2.27897,0.529001,0.282922,0.597792,0.307642,0.459366,0.541549,0.340293,0.265117,0.415364,1.47235,1.22101,0.237549,0.346342,0.684981,1.49721,0.117127,0.941629,1.09491,0.595623,0.350547,2.36682,0.897759,0.561701,0.905643,2.51267,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,1.98793,1.38987,0.4462,0.232216,0.744055,1.0929,1.6127,0.971313,0.156354,0.782748,0.850825,0.424224,0.200147,0.798651,0.625403,0.229431,1.04131,6.11868,3.57827,0.448771,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,0.194299,0.924148,0.715799,0.413337,0.28424,0.875714,0.918549,0.831244,0.753567,1.23455,0.815341,0.589207,1.92716,1.57162,0.395884,0.915771,0.379203,0.507004,1.22894,0.821533,4.31683,2.07616,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,1.33119,1.16062,6.03552,1.0153,0.216774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,2.75549,0.7715,3.74231,0.24928,1.46724,1.92424
|tfbs_overrepresentation_jaspar=MA0003.1;2.91486,MA0004.1;0.502801,MA0006.1;0.341337,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;6.29268,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;1.8235,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;2.46167,MA0056.1;0,MA0057.1;0.744639,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;1.86058,MA0061.1;0.575931,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;0.0022316,MA0074.1;2.49417,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;0.405093,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;0.347695,MA0103.1;0.332048,MA0105.1;0.340955,MA0106.1;5.14579,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;0.277571,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,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;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;0.0807715,MA0146.1;0.0610556,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;0.243958,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.36398,MA0104.2;1.19136,MA0047.2;0.636643,MA0112.2;1.95102,MA0065.2;0.282161,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.335384,MA0155.1;1.89358,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;2.15752,MA0160.1;0.543522,MA0161.1;0,MA0162.1;3.0847,MA0163.1;5.04376,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;3.31082,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:42, 22 January 2013


Full id: C1108_Chondrocyte_Adipocyte_tenocyte_Preadipocyte_Osteoblast_mesenchymal_Myoblast



Phase1 CAGE Peaks

Hg19::chr10:124220985..124220996,+p5@HTRA1
Hg19::chr10:124221036..124221047,+p4@HTRA1
Hg19::chr10:124221061..124221080,+p2@HTRA1
Hg19::chr10:124221082..124221140,+p1@HTRA1
Hg19::chr10:124221146..124221166,+p3@HTRA1
Hg19::chr10:124248410..124248428,+p@chr10:124248410..124248428
+
Hg19::chr10:124248461..124248481,+p7@HTRA1


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
fibroblast5.10e-1376
fat cell3.94e-0915
preadipocyte1.40e-0712
muscle precursor cell1.71e-0758
myoblast1.71e-0758
multi-potent skeletal muscle stem cell1.71e-0758
contractile cell4.57e-0759
non-terminally differentiated cell5.24e-07106
Uber Anatomy
Ontology termp-valuen
multi-cellular organism1.90e-19656
anatomical system5.10e-17624
multi-tissue structure1.01e-16342
anatomical group1.03e-16625
cell layer2.70e-14309
epithelium3.20e-14306
structure with developmental contribution from neural crest3.92e-14132
ecto-epithelium1.00e-13104
neural tube2.06e-1356
neural rod2.06e-1356
future spinal cord2.06e-1356
neural keel2.06e-1356
regional part of nervous system1.30e-1253
regional part of brain1.30e-1253
ectoderm-derived structure1.80e-12171
ectoderm1.80e-12171
presumptive ectoderm1.80e-12171
central nervous system2.04e-1281
brain6.99e-1268
future brain6.99e-1268
neural plate9.83e-1282
presumptive neural plate9.83e-1282
anatomical cluster1.10e-11373
embryonic structure1.68e-11564
developing anatomical structure3.67e-11581
germ layer4.74e-11560
germ layer / neural crest4.74e-11560
embryonic tissue4.74e-11560
presumptive structure4.74e-11560
germ layer / neural crest derived structure4.74e-11560
epiblast (generic)4.74e-11560
regional part of forebrain7.06e-1141
forebrain7.06e-1141
anterior neural tube7.06e-1141
future forebrain7.06e-1141
embryo2.46e-10592
anatomical conduit3.23e-10240
nervous system8.86e-1089
neurectoderm1.00e-0986
adult organism1.41e-09114
telencephalon2.64e-0934
brain grey matter2.85e-0934
gray matter2.85e-0934
dense mesenchyme tissue4.00e-0973
organ4.44e-09503
tube7.59e-09192
surface structure8.20e-0999
pre-chordal neural plate8.27e-0961
paraxial mesoderm9.92e-0972
presumptive paraxial mesoderm9.92e-0972
multilaminar epithelium1.02e-0883
regional part of telencephalon1.34e-0832
organ part1.46e-08218
cerebral hemisphere1.54e-0832
epithelial vesicle1.71e-0878
somite1.88e-0871
presomitic mesoderm1.88e-0871
presumptive segmental plate1.88e-0871
dermomyotome1.88e-0871
trunk paraxial mesoderm1.88e-0871
adipose tissue3.96e-0814
tissue5.37e-08773
organ system subdivision1.18e-07223
integument1.46e-0746
integumental system1.46e-0746
mesenchyme4.57e-07160
entire embryonic mesenchyme4.57e-07160
muscle tissue5.00e-0764
musculature5.00e-0764
musculature of body5.00e-0764
skeletal muscle tissue5.28e-0762
striated muscle tissue5.28e-0762
myotome5.28e-0762
organism subdivision9.68e-07264


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)
MA0003.12.91486
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.16.29268
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
MA0048.11.8235
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.12.46167
MA0056.10
MA0057.10.744639
MA0058.10.406232
MA0059.10.404929
MA0060.11.86058
MA0061.10.575931
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.0022316
MA0074.12.49417
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
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
MA0101.10.347695
MA0103.10.332048
MA0105.10.340955
MA0106.15.14579
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.11.71579
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.0807715
MA0146.10.0610556
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.243958
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.21.19136
MA0047.20.636643
MA0112.21.95102
MA0065.20.282161
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.11.89358
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.12.15752
MA0160.10.543522
MA0161.10
MA0162.13.0847
MA0163.15.04376
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.23.31082
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#186953.505278010628090.005090553587915050.0236826729996107



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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