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Coexpression cluster:C540: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.144412,0.000333902,0.139625,0.678862,0.364884,0.675949,0.300393,0.0518257,0.189397,0.00242338,0.218065,0.335828,0.137255,0.291158,0.112824,0.3998,0.489874,0.0827014,0.151825,0.0465461,0.431825,0.0665914,0.234854,1.18916,0.170101,0.354732,0.0273046,0.233219,0.115495,0.0226422,0.202067,0.522822,0.0662338,0.0349618,0.0937035,0.00978332,0.0919402,0.241614,0.574398,0.04349,1.57903,0.190375,0.323893,2.376,0.00338453,0.15988,0.301272,0.21008,0.292932,0.115573,0.366671,0.310813,0.0632877,0.592653,0.734926,0.293507,0.757014,0.267557,0.0979814,0.266768,0.559896,0.303183,0.0509632,0.465305,0.317765,0.4351,0.818746,1.17567,0.513487,1.01727,0.181085,0.0543134,0.0128276,0.73304,0.0326098,0.118275,0.104456,0.450429,0.510572,0.165891,0.647118,1.17309,1.53638,0.0530449,0.684728,0.00542149,0.045598,0.021314,0.38876,1.27332,0.90828,0.659533,1.33027,0.897208,0.114084,0.947698,0.346672,0.576706,0.392699,0.389681,0.274502,2.26929,0.571612,0.493139,0.425079,0.214722,0.479058,0.288402,0.169928,0.104263,0.146911,0.569087,0.136085,0.225069,0.862131,0.631548,0.0298336,0.201199,0.433061,0.908139,0.725237,1.00454,0.23864,0.326716,0.968805,0.451097,0.295287,0.542501,0.765493,0.265268,0.660176,0.204142,0.779127,4.24617,0.920697,0.0869056,0.19775,0.233646,0.879842,1.7239,1.32497,0.844052,0.296675,2.40187,0.426604,0.260955,0.412168,1.56567,0.188015,0.0681329,0.0107783,0.00407349,0.660531,0.047435,0.302791,1.04704,0.374997,0.699176,0.170141,0.150717,0.842888,0.643319,0.509866,0.152845,1.96266,0.316832,0.0623453,0.299321,0.000933382
|tfbs_overrepresentation_jaspar=MA0003.1;1.09804e-06,MA0004.1;0.221943,MA0006.1;0.362024,MA0007.1;0.208008,MA0009.1;0.621697,MA0014.1;0.000129423,MA0017.1;0.425352,MA0019.1;0.340029,MA0024.1;0.525161,MA0025.1;0.747404,MA0027.1;2.20546,MA0028.1;0.122394,MA0029.1;0.542771,MA0030.1;1.31824,MA0031.1;1.19386,MA0038.1;0.302644,MA0040.1;0.548121,MA0041.1;0.664972,MA0042.1;0.608306,MA0043.1;0.621991,MA0046.1;0.611559,MA0048.1;0.0140676,MA0050.1;0.212584,MA0051.1;0.299199,MA0052.1;0.551663,MA0055.1;0.00123747,MA0056.1;0,MA0057.1;0.0128587,MA0058.1;0.153757,MA0059.1;0.15289,MA0060.1;0.0509127,MA0061.1;0.0397345,MA0063.1;0,MA0066.1;0.302992,MA0067.1;0.924196,MA0068.1;0.0264141,MA0069.1;0.607975,MA0070.1;0.597583,MA0071.1;0.27142,MA0072.1;0.593415,MA0073.1;6.77221e-09,MA0074.1;0.298586,MA0076.1;0.164578,MA0077.1;0.586275,MA0078.1;0.995054,MA0081.1;0.465308,MA0083.1;0.628701,MA0084.1;1.10674,MA0087.1;1.44255,MA0088.1;0.00460154,MA0089.1;0,MA0090.1;0.174619,MA0091.1;0.223914,MA0092.1;0.195947,MA0093.1;0.114388,MA0095.1;0,MA0098.1;0,MA0100.1;0.314026,MA0101.1;0.116395,MA0103.1;0.34743,MA0105.1;0.0103933,MA0106.1;0.33677,MA0107.1;0.0748038,MA0108.2;0.471286,MA0109.1;0,MA0111.1;0.184188,MA0113.1;0.350573,MA0114.1;0.072201,MA0115.1;0.850405,MA0116.1;0.0765991,MA0117.1;0.656858,MA0119.1;0.142224,MA0122.1;0.681203,MA0124.1;0.810546,MA0125.1;0.730403,MA0130.1;0,MA0131.1;0.398042,MA0132.1;0,MA0133.1;0,MA0135.1;0.650071,MA0136.1;0.30842,MA0139.1;0.0351037,MA0140.1;0.74193,MA0141.1;0.151722,MA0142.1;0.445733,MA0143.1;0.350722,MA0144.1;0.0651126,MA0145.1;0.0322091,MA0146.1;7.9117e-05,MA0147.1;0.269778,MA0148.1;0.676348,MA0149.1;0.261654,MA0062.2;0.148712,MA0035.2;0.740647,MA0039.2;0.000177053,MA0138.2;0.38342,MA0002.2;0.0459391,MA0137.2;0.398112,MA0104.2;0.420925,MA0047.2;1.56898,MA0112.2;0.00512484,MA0065.2;0.098884,MA0150.1;0.98029,MA0151.1;0,MA0152.1;0.274535,MA0153.1;0.714423,MA0154.1;0.00994595,MA0155.1;0.025611,MA0156.1;0.12788,MA0157.1;1.08073,MA0158.1;0,MA0159.1;0.270712,MA0160.1;0.703717,MA0161.1;0,MA0162.1;0.000394937,MA0163.1;0.000152387,MA0164.1;0.361105,MA0080.2;0.11444,MA0018.2;0.337929,MA0099.2;0.754549,MA0079.2;7.13602e-15,MA0102.2;1.14323,MA0258.1;0.0605489,MA0259.1;0.28219,MA0442.1;0
}}
}}

Revision as of 19:15, 22 January 2013


Full id: C540_tenocyte_Chondrocyte_Adipocyte_normal_Synoviocyte_Fibroblast_heart



Phase1 CAGE Peaks

Hg19::chr12:91539701..91539744,-p@chr12:91539701..91539744
-
Hg19::chr12:91539859..91539910,-p@chr12:91539859..91539910
-
Hg19::chr12:91539918..91539946,-p@chr12:91539918..91539946
-
Hg19::chr12:91545551..91545568,-p@chr12:91545551..91545568
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Hg19::chr12:91546941..91546972,-p10@DCN
Hg19::chr12:91550883..91550925,-p@chr12:91550883..91550925
-
Hg19::chr12:91552107..91552118,-p@chr12:91552107..91552118
-
Hg19::chr12:91552211..91552251,-p@chr12:91552211..91552251
-
Hg19::chr12:91558446..91558493,-p@chr12:91558446..91558493
-
Hg19::chr12:91572143..91572274,-p6@DCN
Hg19::chr12:91572278..91572327,-p9@DCN
Hg19::chr12:91572389..91572404,-p14@DCN
Hg19::chr12:91573013..91573042,-p@chr12:91573013..91573042
-
Hg19::chr12:91573228..91573245,-p4@DCN
Hg19::chr12:91573249..91573308,-p2@DCN
Hg19::chr12:91573316..91573365,-p3@DCN
Hg19::chr6:125573037..125573043,+p@chr6:125573037..125573043
+


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
fibroblast5.69e-1776
fat cell1.67e-0915
preadipocyte5.38e-0812
skin fibroblast8.34e-0823
GAG secreting cell9.07e-079
carbohydrate secreting cell9.07e-079
Uber Anatomy
Ontology termp-valuen
surface structure5.65e-1099
tissue9.76e-10773
primary circulatory organ1.83e-0927
adult organism1.01e-08114
heart5.78e-0824
primitive heart tube5.78e-0824
primary heart field5.78e-0824
anterior lateral plate mesoderm5.78e-0824
heart tube5.78e-0824
heart primordium5.78e-0824
cardiac mesoderm5.78e-0824
cardiogenic plate5.78e-0824
heart rudiment5.78e-0824
adipose tissue6.18e-0814
multi-cellular organism1.62e-07656
mesenchyme5.85e-07160
entire embryonic mesenchyme5.85e-07160
dense mesenchyme tissue7.15e-0773
integument7.69e-0746
integumental system7.69e-0746


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)
MA0003.11.09804e-06
MA0004.10.221943
MA0006.10.362024
MA0007.10.208008
MA0009.10.621697
MA0014.10.000129423
MA0017.10.425352
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.10.122394
MA0029.10.542771
MA0030.11.31824
MA0031.11.19386
MA0038.10.302644
MA0040.10.548121
MA0041.10.664972
MA0042.10.608306
MA0043.10.621991
MA0046.10.611559
MA0048.10.0140676
MA0050.10.212584
MA0051.10.299199
MA0052.10.551663
MA0055.10.00123747
MA0056.10
MA0057.10.0128587
MA0058.10.153757
MA0059.10.15289
MA0060.10.0509127
MA0061.10.0397345
MA0063.10
MA0066.10.302992
MA0067.10.924196
MA0068.10.0264141
MA0069.10.607975
MA0070.10.597583
MA0071.10.27142
MA0072.10.593415
MA0073.16.77221e-09
MA0074.10.298586
MA0076.10.164578
MA0077.10.586275
MA0078.10.995054
MA0081.10.465308
MA0083.10.628701
MA0084.11.10674
MA0087.11.44255
MA0088.10.00460154
MA0089.10
MA0090.10.174619
MA0091.10.223914
MA0092.10.195947
MA0093.10.114388
MA0095.10
MA0098.10
MA0100.10.314026
MA0101.10.116395
MA0103.10.34743
MA0105.10.0103933
MA0106.10.33677
MA0107.10.0748038
MA0108.20.471286
MA0109.10
MA0111.10.184188
MA0113.10.350573
MA0114.10.072201
MA0115.10.850405
MA0116.10.0765991
MA0117.10.656858
MA0119.10.142224
MA0122.10.681203
MA0124.10.810546
MA0125.10.730403
MA0130.10
MA0131.10.398042
MA0132.10
MA0133.10
MA0135.10.650071
MA0136.10.30842
MA0139.10.0351037
MA0140.10.74193
MA0141.10.151722
MA0142.10.445733
MA0143.10.350722
MA0144.10.0651126
MA0145.10.0322091
MA0146.17.9117e-05
MA0147.10.269778
MA0148.10.676348
MA0149.10.261654
MA0062.20.148712
MA0035.20.740647
MA0039.20.000177053
MA0138.20.38342
MA0002.20.0459391
MA0137.20.398112
MA0104.20.420925
MA0047.21.56898
MA0112.20.00512484
MA0065.20.098884
MA0150.10.98029
MA0151.10
MA0152.10.274535
MA0153.10.714423
MA0154.10.00994595
MA0155.10.025611
MA0156.10.12788
MA0157.11.08073
MA0158.10
MA0159.10.270712
MA0160.10.703717
MA0161.10
MA0162.10.000394937
MA0163.10.000152387
MA0164.10.361105
MA0080.20.11444
MA0018.20.337929
MA0099.20.754549
MA0079.27.13602e-15
MA0102.21.14323
MA0258.10.0605489
MA0259.10.28219
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

No analysis results for this cluster

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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