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Coexpression cluster:C539: Difference between revisions

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{{Coexpression_clusters
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259,0.0860505,0.14446,0.0448633|tfbs_overrepresentation_for_novel_motifs=0.144412,0.011459,0.139625,0.241986,0.11364,0.240734,0.300393,0.192644,0.42191,0.574634,0.622824,0.89216,0.137255,0.291158,0.362746,0.3998,0.489874,0.590721,0.983369,0.710416,0.431825,0.0211682,0.234854,0.356918,0.507569,0.934146,1.18755,0.233219,0.369737,0.0226422,0.202067,0.522822,0.235149,0.326663,0.0937035,3.18307,0.0919402,0.241614,0.574398,0.37945,0.0929322,0.190375,0.178207,0.111922,0.161074,0.15988,0.814646,0.603923,0.15881,0.115573,0.366671,0.310813,0.167715,0.592653,0.734926,0.293507,0.376618,0.267557,0.0979814,0.266768,0.559896,0.303183,0.190033,0.465305,0.317765,0.4351,0.818746,1.17567,0.513487,1.01727,0.534356,0.442034,0.550473,0.73304,0.0326098,0.283688,0.25554,0.450429,0.510572,0.497229,1.00731,2.04237,0.851126,0.43491,0.684728,0.000729711,0.00893619,1.44974,0.38876,1.27332,0.90828,1.58578,0.537982,0.245209,0.738776,0.263897,0.150074,0.576706,0.392699,0.0784744,0.577898,0.532876,0.571612,2.13824,0.425079,0.214722,0.479058,0.785497,1.55549,0.340143,0.882247,0.569087,0.422755,0.225069,0.862131,0.304665,0.00825856,0.201199,1.93711,0.0711462,0.725237,0.386689,0.671072,0.326716,0.968805,0.451097,1.45664,0.542501,0.765493,0.0768182,1.58712,0.204142,0.779127,0.323981,0.920697,0.68611,0.19775,0.233646,0.879842,1.7239,1.32497,0.844052,0.296675,0.573485,0.426604,1.33087,0.412168,1.56567,0.188015,0.0681329,0.0107783,0.00407349,0.660531,0.179266,1.48373,1.04704,0.374997,0.343221,0.507668,0.150717,0.842888,0.643319,0.509866,0.152845,1.12193,0.849678,0.486038,0.299321,0.000163633|tfbs_overrepresentation_jaspar=MA0003.1;0.0256099,MA0004.1;0.221943,MA0006.1;0.112549,MA0007.1;0.208008,MA0009.1;0.621697,MA0014.1;0.00547893,MA0017.1;0.137108,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;0.532314,MA0031.1;0.474026,MA0038.1;0.302644,MA0040.1;1.35175,MA0041.1;0.236024,MA0042.1;0.211928,MA0043.1;1.5073,MA0046.1;0.611559,MA0048.1;0.174542,MA0050.1;0.609862,MA0051.1;1.47078,MA0052.1;0.551663,MA0055.1;0.624776,MA0056.1;0,MA0057.1;0.551171,MA0058.1;0.153757,MA0059.1;0.15289,MA0060.1;0.422819,MA0061.1;0.0397345,MA0063.1;0,MA0066.1;0.302992,MA0067.1;0.924196,MA0068.1;0.803993,MA0069.1;0.607975,MA0070.1;0.597583,MA0071.1;0.27142,MA0072.1;0.593415,MA0073.1;2.4855,MA0074.1;0.298586,MA0076.1;0.164578,MA0077.1;1.43229,MA0078.1;0.382364,MA0081.1;0.907903,MA0083.1;0.628701,MA0084.1;1.10674,MA0087.1;0.591148,MA0088.1;0.755104,MA0089.1;0,MA0090.1;0.518617,MA0091.1;0.636604,MA0092.1;0.195947,MA0093.1;0.114388,MA0095.1;0,MA0098.1;0,MA0100.1;0.314026,MA0101.1;0.116395,MA0103.1;0.706501,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;0.25223,MA0115.1;0.850405,MA0116.1;0.264652,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;0.269307,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;0.0784275,MA0148.1;0.240905,MA0149.1;0.261654,MA0062.2;0.0377014,MA0035.2;0.268747,MA0039.2;0.00741171,MA0138.2;0.38342,MA0002.2;0.174654,MA0137.2;0.126444,MA0104.2;0.0505812,MA0047.2;0.326636,MA0112.2;0.08608,MA0065.2;1.17085,MA0150.1;0.170499,MA0151.1;0,MA0152.1;0.274535,MA0153.1;0.714423,MA0154.1;0.00994595,MA0155.1;0.0782503,MA0156.1;0.12788,MA0157.1;0.421609,MA0158.1;0,MA0159.1;0.270712,MA0160.1;0.252705,MA0161.1;0,MA0162.1;0.000394937,MA0163.1;0.166772,MA0164.1;0.948242,MA0080.2;0.366978,MA0018.2;0.337929,MA0099.2;0.27482,MA0079.2;0.296572,MA0102.2;1.14323,MA0258.1;0.0605489,MA0259.1;0.28219,MA0442.1;0}}
|full_id=C539_teratocarcinoma_diffuse_Gingival_Placental_lymphangiectasia_mycosis_Sebocyte
|id=C539
}}

Latest revision as of 11:25, 17 September 2013


Full id: C539_teratocarcinoma_diffuse_Gingival_Placental_lymphangiectasia_mycosis_Sebocyte



Phase1 CAGE Peaks

Hg19::chr12:4382904..4382916,+p4@CCND2
Hg19::chr12:4382917..4382935,+p1@CCND2
Hg19::chr12:4382956..4382975,+p2@CCND2
Hg19::chr12:4382987..4383001,+p3@CCND2
Hg19::chr12:4409051..4409087,+p7@CCND2
Hg19::chr12:4409178..4409221,+p5@CCND2
Hg19::chr12:4409319..4409336,-p@chr12:4409319..4409336
-
Hg19::chr12:4409925..4409954,+p@chr12:4409925..4409954
+
Hg19::chr12:4409972..4409984,+p@chr12:4409972..4409984
+
Hg19::chr12:4410530..4410541,+p@chr12:4410530..4410541
+
Hg19::chr12:4410648..4410662,+p@chr12:4410648..4410662
+
Hg19::chr12:4410859..4410873,+p@chr12:4410859..4410873
+
Hg19::chr12:4411116..4411133,+p@chr12:4411116..4411133
+
Hg19::chr12:4412433..4412455,+p@chr12:4412433..4412455
+
Hg19::chr12:4413412..4413423,+p10@CCND2
Hg19::chr12:4413888..4413949,+p@chr12:4413888..4413949
+
Hg19::chr12:4414171..4414189,+p@chr12:4414171..4414189
+


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>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism1.42e-09114
cerebral cortex1.20e-0725
pallium1.20e-0725
brain grey matter1.54e-0734
gray matter1.54e-0734
cerebral hemisphere1.77e-0732
telencephalon2.39e-0734
regional part of forebrain2.48e-0741
forebrain2.48e-0741
anterior neural tube2.48e-0741
future forebrain2.48e-0741
regional part of telencephalon2.52e-0732
neural tube4.95e-0756
neural rod4.95e-0756
future spinal cord4.95e-0756
neural keel4.95e-0756
regional part of cerebral cortex6.71e-0722
ecto-epithelium9.87e-07104


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)
MA0003.10.0256099
MA0004.10.221943
MA0006.10.112549
MA0007.10.208008
MA0009.10.621697
MA0014.10.00547893
MA0017.10.137108
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.10.122394
MA0029.10.542771
MA0030.10.532314
MA0031.10.474026
MA0038.10.302644
MA0040.11.35175
MA0041.10.236024
MA0042.10.211928
MA0043.11.5073
MA0046.10.611559
MA0048.10.174542
MA0050.10.609862
MA0051.11.47078
MA0052.10.551663
MA0055.10.624776
MA0056.10
MA0057.10.551171
MA0058.10.153757
MA0059.10.15289
MA0060.10.422819
MA0061.10.0397345
MA0063.10
MA0066.10.302992
MA0067.10.924196
MA0068.10.803993
MA0069.10.607975
MA0070.10.597583
MA0071.10.27142
MA0072.10.593415
MA0073.12.4855
MA0074.10.298586
MA0076.10.164578
MA0077.11.43229
MA0078.10.382364
MA0081.10.907903
MA0083.10.628701
MA0084.11.10674
MA0087.10.591148
MA0088.10.755104
MA0089.10
MA0090.10.518617
MA0091.10.636604
MA0092.10.195947
MA0093.10.114388
MA0095.10
MA0098.10
MA0100.10.314026
MA0101.10.116395
MA0103.10.706501
MA0105.10.0103933
MA0106.10.33677
MA0107.10.0748038
MA0108.20.471286
MA0109.10
MA0111.10.184188
MA0113.10.350573
MA0114.10.25223
MA0115.10.850405
MA0116.10.264652
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
MA0140.10.269307
MA0141.10.151722
MA0142.10.445733
MA0143.10.350722
MA0144.10.0651126
MA0145.10.0322091
MA0146.17.9117e-05
MA0147.10.0784275
MA0148.10.240905
MA0149.10.261654
MA0062.20.0377014
MA0035.20.268747
MA0039.20.00741171
MA0138.20.38342
MA0002.20.174654
MA0137.20.126444
MA0104.20.0505812
MA0047.20.326636
MA0112.20.08608
MA0065.21.17085
MA0150.10.170499
MA0151.10
MA0152.10.274535
MA0153.10.714423
MA0154.10.00994595
MA0155.10.0782503
MA0156.10.12788
MA0157.10.421609
MA0158.10
MA0159.10.270712
MA0160.10.252705
MA0161.10
MA0162.10.000394937
MA0163.10.166772
MA0164.10.948242
MA0080.20.366978
MA0018.20.337929
MA0099.20.27482
MA0079.20.296572
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ATF3#46745.285452829649120.005857629621042940.0262955074142318
BATF#1053845.731247480542030.004394533429899440.020824932024378
CTBP2#1488414.75694125631250.000130022472899810.00171068493917653



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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