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Coexpression cluster:C2272: Difference between revisions

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{{Coexpression_clusters
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49,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.0585101,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.298605,0.581696,1.75588,0.534346,0.739643,0.821651,0.395818,0.392841,2.07992,2.82941,0.867962,1.62243,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,0.849366,0.728867,0.537869,1.46495,0.682839,1.09415,1.10579,0.344471,1.23824,0.0842336,2.13139,0.740899,0.463978,0.371755,1.23481,0.66492,0.183156,0.53106,0.648765,0.61613,1.92371,1.65941,0.99221,1.33034,0.90714,1.94963,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,1.8276,4.16336,0.825354,1.0193,1.02706,0.844545,2.26787,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,5.56341,1.32819,0.893276,0.859396,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,4.58731,8.09613,5.26138,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,1.37313,0.465545,1.1057,2.59018,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.393155,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.774456,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,3.82793,1.24902,0.383416,1.92786,1.65997,0.917558,1.28873,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,1.90479,0.820225,0.0401987|tfbs_overrepresentation_jaspar=MA0003.1;0.720743,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.896009,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;4.04183,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.791759,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;2.64938,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.00636811,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;1.33363,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.569905,MA0146.1;0.061409,MA0147.1;1.16748,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;2.51225,MA0035.2;0.778873,MA0039.2;0.0247757,MA0138.2;0.928035,MA0002.2;0.98779,MA0137.2;0.558189,MA0104.2;1.79838,MA0047.2;0.856092,MA0112.2;0.551048,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;1.84959,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.180766,MA0156.1;2.36058,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;3.50007,MA0163.1;0.539587,MA0164.1;0.90014,MA0080.2;1.32578,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.327251,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;1.1888,MA0442.1;0}}
|full_id=C2272_amniotic_chorionic_oral_glassy_colon_epidermoid_Mallassezderived
|id=C2272
}}

Latest revision as of 12:02, 17 September 2013


Full id: C2272_amniotic_chorionic_oral_glassy_colon_epidermoid_Mallassezderived



Phase1 CAGE Peaks

Hg19::chr13:80055378..80055401,+p5@NDFIP2
Hg19::chr13:80055403..80055426,+p1@NDFIP2
Hg19::chr13:80055432..80055449,+p4@NDFIP2
Hg19::chr13:80055462..80055478,+p6@NDFIP2


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>disease_data<br>

Cell Type
Ontology termp-valuen
endo-epithelial cell2.69e-1442
endodermal cell1.05e-1258
epithelial cell of alimentary canal8.33e-1120
epithelial cell3.18e-10253
Uber Anatomy
Ontology termp-valuen
organ system subdivision1.69e-21223
multi-tissue structure5.11e-19342
organ part2.47e-16218
organ2.28e-15503
ectoderm-derived structure5.14e-15171
ectoderm5.14e-15171
presumptive ectoderm5.14e-15171
anatomical cluster5.47e-15373
endoderm-derived structure3.29e-14160
endoderm3.29e-14160
presumptive endoderm3.29e-14160
regional part of forebrain1.19e-1241
forebrain1.19e-1241
anterior neural tube1.19e-1241
future forebrain1.19e-1241
ecto-epithelium2.27e-12104
telencephalon4.90e-1234
neural tube8.51e-1256
neural rod8.51e-1256
future spinal cord8.51e-1256
neural keel8.51e-1256
regional part of nervous system1.25e-1153
regional part of brain1.25e-1153
cerebral hemisphere1.43e-1132
digestive system1.51e-11145
digestive tract1.51e-11145
primitive gut1.51e-11145
anatomical system2.76e-11624
brain grey matter2.81e-1134
gray matter2.81e-1134
regional part of telencephalon3.53e-1132
anatomical group3.67e-11625
multi-cellular organism8.15e-11656
brain2.65e-1068
future brain2.65e-1068
subdivision of digestive tract3.34e-10118
regional part of cerebral cortex4.42e-1022
central nervous system6.33e-1081
nervous system1.18e-0989
epithelium1.20e-09306
neocortex3.07e-0920
cell layer3.44e-09309
cerebral cortex1.33e-0825
pallium1.33e-0825
organ component layer1.80e-0866
surface structure1.87e-0899
pre-chordal neural plate2.46e-0861
neural plate3.36e-0882
presumptive neural plate3.36e-0882
adult organism1.33e-07114
neurectoderm2.04e-0786
structure with developmental contribution from neural crest2.97e-07132
developing anatomical structure3.73e-07581
embryo4.27e-07592
anatomical conduit5.34e-07240
extraembryonic membrane8.47e-0714
membranous layer8.47e-0714
Disease
Ontology termp-valuen
cell type cancer4.74e-08143
carcinoma7.07e-08106
female reproductive organ cancer3.85e-0727
reproductive organ cancer5.09e-0729


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)
MA0003.10.720743
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.896009
MA0017.10.577281
MA0019.10.873355
MA0024.14.04183
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.12.64938
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.10.061409
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.22.51225
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.21.79838
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.11.84959
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.12.36058
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.13.50007
MA0163.10.539587
MA0164.10.90014
MA0080.21.32578
MA0018.20.870662
MA0099.20.7872
MA0079.20.327251
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
CCNT2#90546.336201576962630.0006203100587215640.0051156476802607
E2F1#186944.907389214879320.001724022357361790.010633388707288
E2F6#187645.017155731697390.00157802193473060.00995632410084752
EGR1#195844.988179094810140.001615011500076050.0101321671205889
ELF1#199744.258097958807540.003041525565781240.0160674703371081
ELK4#2005416.2356816584681.43847748454449e-050.000343076387322087
ETS1#211349.728760922202340.0001115955317418140.00154369877345474
GABPB1#255347.067683836182170.0004006876864423170.00389931245661099
HEY1#2346244.040111043105710.00375304636917980.0185694717524526
HMGN3#932448.178547723350590.0002234570284440470.002477981375416
IRF1#365947.63716375356390.0002938853996185490.00307053794025226
MYC#460945.22228187160940.001344309395272740.00886353086697534
NFKB1#479045.488063424193840.001102199566301980.00767161749450265
NRF1#4899412.21027944771094.49717228915276e-050.00079257539100038
PAX5#507946.669565531177830.0005052774169483260.00443376475791179
POU2F2#545249.106124057742520.000145395665174930.00188212417888008
SIN3A#2594245.408884726815140.001168172384885160.00795013395705857
SPI1#668848.204323508522730.000220661881527680.00249304481229656
TAF1#687243.343046285745290.008005664898701650.0321565953753895
TBP#690843.706770687096390.005296377814784350.0243720656766947
ZEB1#6935416.88843201754391.22862303393937e-050.000303635023761462
ZNF263#1012748.221841637010680.0002187871180958320.00248233653740474



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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