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Coexpression cluster:C2909: Difference between revisions

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{{Coexpression_clusters
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0.0612213,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.0567862,0.15156,0.00505104,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.0604859,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.0133959,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.0472356,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.003871,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.00786668,0.410951,0.289049,0.266974,0.00825997,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.045178,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=1.44014,0.298605,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,1.68405,0.867962,0.341754,1.89595,0.532789,0.559384,1.05593,0.471262,0.356737,1.18986,0.581762,0.975621,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,1.33003,2.23762,0.682839,2.47734,0.433165,0.344471,0.49475,0.0842336,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,0.0946706,1.49501,1.92371,1.65941,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,1.82985,0.297448,0.776148,1.13655,0.825354,0.393426,2.3411,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,1.5667,0.402607,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,1.51572,1.69485,1.02594,0.844168,0.399165,1.27559,0.109222,1.18341,2.2083,2.1528,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,1.15724,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,5.43215,3.87745,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,2.30681,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,1.62065,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,2.59446,5.24689,0.768101,0.963351,2.1895,0.661255,1.11576,1.23342,0.521611,1.24902,4.69098,0.824835,1.65997,0.917558,3.27439,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.156682|tfbs_overrepresentation_jaspar=MA0003.1;0.233555,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;6.80202,MA0009.1;1.20602,MA0014.1;0.244769,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;4.60325,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;1.92746,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.709734,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,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;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.100363,MA0074.1;0.819248,MA0076.1;2.5647,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;1.6149,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;1.9583,MA0101.1;0.539569,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;1.09982,MA0145.1;0.195821,MA0146.1;0.221129,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;1.66396,MA0035.2;0.778873,MA0039.2;0.483275,MA0138.2;2.1393,MA0002.2;0.379056,MA0137.2;2.35208,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;1.02191,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.640035,MA0163.1;0.253219,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.000248021,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2909_lymphoma_adenocarcinoma_chronic_acute_diffuse_nonsmall_CD19
|id=C2909
|ontology_enrichment_celltype=CL:0000542!3.06e-08!53;CL:0000051!3.06e-08!53;CL:0000838!8.98e-08!52
|ontology_enrichment_disease=DOID:2531!8.54e-23!51;DOID:0060083!8.54e-23!51;DOID:162!8.36e-22!235;DOID:14566!3.59e-20!239;DOID:1240!5.57e-18!39;DOID:8692!1.73e-14!31;DOID:0050686!9.18e-14!137;DOID:0050687!3.29e-11!143;DOID:305!6.75e-11!106
|ontology_enrichment_uberon=
}}

Latest revision as of 12:15, 17 September 2013


Full id: C2909_lymphoma_adenocarcinoma_chronic_acute_diffuse_nonsmall_CD19



Phase1 CAGE Peaks

Hg19::chr7:96746988..96747028,+p1@ACN9
Hg19::chr7:96747030..96747041,+p4@ACN9
Hg19::chr7:96747044..96747055,+p3@ACN9
Hg19::chr7:96747057..96747073,+p2@ACN9


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><br>disease_data<br>

Cell Type
Ontology termp-valuen
nucleate cell4.99e-0855
lymphocyte1.34e-0753
common lymphoid progenitor1.34e-0753
lymphoid lineage restricted progenitor cell3.74e-0752
Disease
Ontology termp-valuen
hematologic cancer1.45e-2251
immune system cancer1.45e-2251
cancer3.87e-22235
disease of cellular proliferation2.61e-20239
leukemia9.46e-1839
organ system cancer9.24e-15137
myeloid leukemia1.61e-1431
carcinoma1.65e-10106
cell type cancer2.01e-10143


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)
MA0003.10.233555
MA0004.10.71247
MA0006.10.532262
MA0007.16.80202
MA0009.11.20602
MA0014.10.244769
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.14.60325
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.11.92746
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
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
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.100363
MA0074.10.819248
MA0076.12.5647
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
MA0092.11.6149
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.11.9583
MA0101.10.539569
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
MA0144.11.09982
MA0145.10.195821
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.20.778873
MA0039.20.483275
MA0138.22.1393
MA0002.20.379056
MA0137.22.35208
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.000248021
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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#602434.54710280373837.01262157705428e-073.15549842691069e-05
BCLAF1#9774421.65264761012184.54636978835329e-060.000141948673938963
CCNT2#90546.336201576962630.0006203100587215640.0051375544982412
CEBPB#105147.971147625824820.0002476385788090830.00268735718331689
CTCF#1066445.360256373075030.001211145381643620.00820144022002712
CTCFL#140690419.74647435897446.5732084880439e-060.000193598229352176
E2F1#186944.907389214879320.001724022357361790.0106813294762121
E2F4#1874412.66806031528443.88145892637771e-050.000728307022658933
E2F6#187645.017155731697390.00157802193473060.00999557452943528
EGR1#195844.988179094810140.001615011500076050.0101682050914181
ELF1#199744.258097958807540.003041525565781240.0161294754018801
ELK4#2005416.2356816584681.43847748454449e-050.000343704301094354
EP300#203346.77394172622320.0004748459821442640.00435518042760734
ETS1#211349.728760922202340.0001115955317418140.0015486215439255
FOS#235348.99795530889440.0001525147711168630.00195537566666757
FOSL1#8061439.7135797163734.01511434669553e-071.94046518859109e-05
GABPB1#255347.067683836182170.0004006876864423170.00390951245182634
GTF2F1#2962412.73966087675773.79492332235515e-050.000719437278750136
HEY1#2346244.040111043105710.00375304636917980.0186658607434054
HMGN3#932448.178547723350590.0002234570284440470.00248616475909959
HNF4A#3172423.13229036295373.48990320893214e-060.000115855690158189
IRF1#365947.63716375356390.0002938853996185490.0030807083459562
IRF4#3662421.91451268674414.33289161192893e-060.000136837879364453
JUN#3725412.51282919233634.07770316866756e-050.000745311937753712
JUND#372746.994663941871030.000417684217818580.00392677306911105
MAX#414946.452555509007120.0005767613195645490.00486719258678102
MEF2A#4205418.74323090964418.0978922767748e-060.000224750404330078
MXI1#460149.96157162875930.0001015224754950450.00142800078359959
MYC#460945.22228187160940.001344309395272740.00890061677018444
NFKB1#479045.488063424193840.001102199566301980.00769469388402489
NRF1#4899412.21027944771094.49717228915276e-050.000795663521441344
PAX5#507946.669565531177830.0005052774169483260.0044498413145009
POU2F2#545249.106124057742520.000145395665174930.00188820913643428
REST#597849.650028716128020.0001152825614219170.00157591563250571
SETDB1#9869440.32002617801053.77887289069054e-071.8537421598442e-05
SIN3A#2594245.408884726815140.001168172384885160.00798290621638558
SIX5#147912417.0867153554591.17257016123224e-050.000297888725538637
SMARCC1#6599443.66335931963152.74744977017458e-071.40795341779815e-05
SP1#666745.69838137814090.0009482606065333980.00685793154807434
SRF#6722413.79717826216782.75840773062708e-050.000585896573070899
STAT3#6774410.51946499715428.16377768286615e-050.00123549743141698
TAF1#687243.343046285745290.008005664898701650.0323381797081996
TAF7#6879411.43306940492395.85061525419808e-050.000972052826174345
TBP#690843.706770687096390.005296377814784350.0245092118657567
TCF7L2#6934410.77017656313737.42969445082454e-050.0011579612874939
THAP1#55145431.36914460285131.03171810326891e-064.32737377459043e-05
TRIM28#10155418.59052504526258.36730015875654e-060.000231122047416127
USF1#739146.361499277207960.0006105011399140830.00509225529522298
YY1#752844.911170749853860.00171871838055440.0107100971925251
ZBTB7A#5134147.35190930787590.000342223540015990.00347341927072206
ZNF263#1012748.221841637010680.0002187871180958320.00250053707888056



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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