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Coexpression cluster:C3176: Difference between revisions

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{{Coexpression_clusters
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8,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.0246892,0.207559,0.000532415,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.00157872,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.018841,0.0297055,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.0232618,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,1.99148,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,1.45286,0.855276,0.567465,0.469078,0.598234,1.82956,0.718382,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,5.1274,0.336258,1.29475,1.45259,2.14035,0.650353,2.06667,0.388177,2.0644,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,1.5923,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,0.303648,1.76229,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,1.54991,0.560075,1.14422,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,3.17067,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,1.05469,0.794219,1.10778,0.547323,1.44203,1.0504,1.98143,0.973172,1.70203,4.14226,0.930979,10.2266,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,3.99678,2.31409,0.773313,1.33389,0.318511,1.29196,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,1.76124,0.710709,5.47603,2.99787,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232|tfbs_overrepresentation_jaspar=MA0003.1;0.178364,MA0004.1;0.826076,MA0006.1;1.5435,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.118426,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;4.40988,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.0185922,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;1.80901,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.107247,MA0147.1;1.38767,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.432958,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;1.60005,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.760954,MA0150.1;1.76247,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;5.17967,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;0.387745,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.0373086,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;1.40979,MA0442.1;0}}
|full_id=C3176_oral_cervical_Esophageal_Hep2_iPS_giant_choriocarcinoma
|id=C3176
}}

Latest revision as of 12:20, 17 September 2013


Full id: C3176_oral_cervical_Esophageal_Hep2_iPS_giant_choriocarcinoma



Phase1 CAGE Peaks

Hg19::chr11:62623512..62623526,+p9@SLC3A2
Hg19::chr11:62623544..62623614,+p3@SLC3A2
Hg19::chr11:62623621..62623640,+p5@SLC3A2


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
epithelial cell6.15e-48253
embryonic cell8.48e-14250
endodermal cell1.26e-1258
endo-epithelial cell1.30e-1142
animal cell7.41e-11679
eukaryotic cell7.41e-11679
squamous epithelial cell1.05e-0963
epithelial cell of lung2.68e-0819
respiratory epithelial cell1.75e-0713
Uber Anatomy
Ontology termp-valuen
respiratory primordium1.31e-0938
endoderm of foregut1.31e-0938
segment of respiratory tract3.60e-0947
respiratory tract2.44e-0854
respiratory tract epithelium2.68e-0819
lung epithelium2.68e-0819
foregut9.88e-0887
larynx1.62e-079
respiratory system9.03e-0774
Disease
Ontology termp-valuen
cancer1.39e-43235
disease of cellular proliferation9.61e-42239
cell type cancer6.96e-32143
carcinoma1.19e-31106
organ system cancer1.26e-16137
hematologic cancer1.98e-0751
immune system cancer1.98e-0751
disease of anatomical entity3.35e-0739
adenocarcinoma9.34e-0725


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)
MA0003.10.178364
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.14.40988
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.11.80901
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.11.76247
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.15.17967
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0373086
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
BCL3#602334.54710280373832.42397750207122e-050.000526315564113963
BCLAF1#9774321.65264761012189.8473954032885e-050.00138848674027818
CCNT2#90536.336201576962630.003930750035764890.0189233706548008
CEBPB#105137.971147625824820.001974187055288560.0114967169547943
CTCFL#140690319.74647435897440.0001298372005551160.00171212972080503
E2F1#186934.907389214879320.008460985347239390.0323778707562778
E2F4#1874312.66806031528440.0004917987006298980.00435685507634965
E2F6#187635.017155731697390.00791769806886330.032058481376057
EBF1#187938.9064668465690.00141523283560980.0091254863319289
EGR1#195834.988179094810140.008056488137383440.0319200138308114
ELF1#199734.258097958807540.01295179875054610.0460233714303114
EP300#203336.77394172622320.003216880500103790.0166932218299881
ESR1#2099330.76860329615453.43136389821584e-050.000674004540465984
ETS1#211339.728760922202340.001085840092584840.00760131734227949
FOSL2#2355316.93020060456170.0002060162053171620.00242380606816707
FOXA1#3169311.08141974938550.000734755275698670.00579629173190523
GABPB1#255337.067683836182170.002832212825417420.0153658948194166
GATA1#2623313.56030814380040.0004009615963782630.00386917011587817
GTF2B#2959331.94382993432423.06634405746243e-050.000625969325678888
GTF2F1#2962312.73966087675770.0004835525047438590.00432785500410866
HDAC2#3066313.41562023662630.0004140761399857210.00389952191018654
HDAC8#558693776.5840336134452.10837623426304e-091.80785472520688e-07
HMGN3#932438.178547723350590.001827766942164210.0108355651741323
HNF4G#3174328.75342252644684.20470658818262e-050.00075504702779093
IRF1#365937.63716375356390.002244692747297240.012765926041983
JUN#3725312.51282919233630.0005103313992726250.00443120227873576
JUND#372736.994663941871030.002921845042734990.015620115398147
MAX#414936.452555509007120.003721913834265510.0185844788170231
MEF2A#4205318.74323090964410.0001518243905622470.00194843788718733
MXI1#460139.96157162875930.001011470541259020.00718374511108813
MYC#460935.22228187160940.007020843755740150.0293288228873143
NANOG#79923329.24477848101273.99627955670032e-050.000734155568376825
NFKB1#479035.488063424193840.006049381815655430.0268664478416924
NRF1#4899312.21027944771090.0005492172401020010.00469661011536992
PAX5#507936.669565531177830.003370290999677260.0172375035120124
POU2F2#545239.106124057742520.001324165192682130.00879791898711934
REST#597839.650028716128020.001112636247114590.00765498135786566
RFX5#5993312.04791082719510.0005717246050312580.0048317159754701
SIN3A#2594235.408884726815140.006318961977991520.0275540090192249
SIX5#147912317.0867153554590.0002004060546325010.00239065767444475
SP1#666735.69838137814090.005403962701712170.024553400356918
SRF#6722313.79717826216780.0003806615025800190.00373997240526384
TAF7#6879311.43306940492390.0006690181981945830.00540759938094916
TCF12#6938310.63446490218640.0008313523990202070.00627851711629701
TCF7L2#6934310.77017656313730.0008003181298398380.00611936636374133
TFAP2C#7022310.80922860986020.0007916746575753130.00613092907923092
THAP1#55145331.36914460285133.23800758564397e-050.000645247613503283
TRIM28#10155318.59052504526250.0001555969297255280.00196569344908726
USF1#739136.361499277207960.00388404057290560.0189589322019858
USF2#7392312.99219738506960.0004558979393427810.00420539877115534
YY1#752834.911170749853860.008441455341808260.0328080215258676
ZBTB7A#5134137.35190930787590.002516255860282270.0139658418340872
ZEB1#6935316.88843201754390.0002075486917327580.00242029676372013
ZNF143#7702313.50087655222790.0004062804962997170.003878213029252



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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