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Coexpression cluster:C2354: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,1.42265,0.741427,0.534346,0.739643,0.821651,0.395818,1.01802,0.902371,0.706765,0.867962,0.341754,1.89595,0.532789,0.559384,1.05593,0.471262,0.356737,2.60868,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,2.28567,3.10169,0.682839,1.09415,1.10579,1.63198,2.14358,1.49582,0.491074,1.75478,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,1.08066,0.61613,1.92371,0.694903,0.515703,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,4.39613,0.297448,0.776148,1.13655,1.92893,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,3.25144,1.49254,1.00941,1.08,2.5716,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,1.44378,0.934646,1.89266,1.51507,1.24792,1.11156,2.92606,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,3.52745,0.717043,1.46636,0.489254,0.12452,3.98826,0.988625,1.1313,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,1.90732,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,1.41398,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,2.24704,0.768101,0.963351,2.1895,0.661255,1.11576,0.234974,0.175846,1.24902,1.76758,0.824835,1.65997,0.917558,0.518428,0.632914,3.63844,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,1.91838,1.4289
|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,1.42265,0.741427,0.534346,0.739643,0.821651,0.395818,1.01802,0.902371,0.706765,0.867962,0.341754,1.89595,0.532789,0.559384,1.05593,0.471262,0.356737,2.60868,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,2.28567,3.10169,0.682839,1.09415,1.10579,1.63198,2.14358,1.49582,0.491074,1.75478,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,1.08066,0.61613,1.92371,0.694903,0.515703,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,4.39613,0.297448,0.776148,1.13655,1.92893,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,3.25144,1.49254,1.00941,1.08,2.5716,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,1.44378,0.934646,1.89266,1.51507,1.24792,1.11156,2.92606,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,3.52745,0.717043,1.46636,0.489254,0.12452,3.98826,0.988625,1.1313,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,1.90732,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,1.41398,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,2.24704,0.768101,0.963351,2.1895,0.661255,1.11576,0.234974,0.175846,1.24902,1.76758,0.824835,1.65997,0.917558,0.518428,0.632914,3.63844,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,1.91838,1.4289
|tfbs_overrepresentation_jaspar=MA0003.1;0.443649,MA0004.1;2.8475,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.0695829,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,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;2.53613,MA0041.1;0.732902,MA0042.1;1.66514,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;3.70332,MA0050.1;2.80362,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;5.70469,MA0056.1;0,MA0057.1;3.6449,MA0058.1;4.90963,MA0059.1;3.65449,MA0060.1;0.393285,MA0061.1;1.68681,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;0.0343867,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;0.536981,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;4.51906,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;1.33363,MA0103.1;1.29536,MA0105.1;0.656404,MA0106.1;0.869173,MA0107.1;2.00595,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;2.78257,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;1.63368,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.481,MA0147.1;3.01834,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.257871,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;2.6968,MA0047.2;0.856092,MA0112.2;5.79077,MA0065.2;0.577908,MA0150.1;1.53138,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;3.02177,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.309472,MA0163.1;0.539587,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;1.85039,MA0079.2;1.38179,MA0102.2;1.75932,MA0258.1;7.34172,MA0259.1;2.06681,MA0442.1;0
}}
}}

Revision as of 20:36, 22 January 2013


Full id: C2354_CD14_Eosinophils_CD19_Reticulocytes_CD4_Smooth_Neutrophils



Phase1 CAGE Peaks

Hg19::chr15:89182156..89182177,+p6@ISG20
Hg19::chr15:89182178..89182202,+p4@ISG20
Hg19::chr15:89182208..89182225,+p5@ISG20
Hg19::chr15:89182240..89182265,+p1@ISG20


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
leukocyte2.87e-34136
nongranular leukocyte7.55e-32115
hematopoietic lineage restricted progenitor cell6.05e-28120
nucleate cell1.21e-2155
hematopoietic cell4.10e-21177
hematopoietic stem cell6.68e-21168
angioblastic mesenchymal cell6.68e-21168
lymphocyte2.25e-2053
common lymphoid progenitor2.25e-2053
lymphoid lineage restricted progenitor cell3.59e-2052
classical monocyte2.26e-1942
CD14-positive, CD16-negative classical monocyte2.26e-1942
hematopoietic oligopotent progenitor cell4.44e-19161
hematopoietic multipotent progenitor cell4.44e-19161
defensive cell2.45e-1448
phagocyte2.45e-1448
lymphocyte of B lineage2.48e-1224
pro-B cell2.48e-1224
myeloid leukocyte1.40e-1172
macrophage dendritic cell progenitor1.59e-1161
monopoietic cell3.61e-1159
monocyte3.61e-1159
monoblast3.61e-1159
promonocyte3.61e-1159
mature alpha-beta T cell4.88e-1018
alpha-beta T cell4.88e-1018
immature T cell4.88e-1018
mature T cell4.88e-1018
immature alpha-beta T cell4.88e-1018
myeloid lineage restricted progenitor cell2.79e-0966
granulocyte monocyte progenitor cell6.05e-0967
B cell1.46e-0814
T cell3.70e-0825
pro-T cell3.70e-0825
CD8-positive, alpha-beta T cell9.49e-0711
Uber Anatomy
Ontology termp-valuen
hemolymphoid system2.26e-14108
hematopoietic system4.82e-1498
blood island4.82e-1498
immune system6.30e-0993
blood9.28e-0915
haemolymphatic fluid9.28e-0915
organism substance9.28e-0915


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)
MA0003.10.443649
MA0004.12.8475
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.12.53613
MA0041.10.732902
MA0042.11.66514
MA0043.11.20635
MA0046.11.19471
MA0048.13.70332
MA0050.12.80362
MA0051.10.820063
MA0052.11.12718
MA0055.15.70469
MA0056.10
MA0057.13.6449
MA0058.14.90963
MA0059.13.65449
MA0060.10.393285
MA0061.11.68681
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.0343867
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.14.51906
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.11.29536
MA0105.10.656404
MA0106.10.869173
MA0107.12.00595
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.12.78257
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
MA0139.11.63368
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.481
MA0147.13.01834
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.22.6968
MA0047.20.856092
MA0112.25.79077
MA0065.20.577908
MA0150.11.53138
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.13.02177
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.21.85039
MA0079.21.38179
MA0102.21.75932
MA0258.17.34172
MA0259.12.06681
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#467422.46317452600873.92475754624726e-060.000127257917843067
BATF#10538424.35780179230362.83869198020713e-069.7748154210634e-05
BCL11A#53335428.36945510360711.542446414682e-065.88784945551804e-05
BCL3#602434.54710280373837.01262157705428e-073.14601024435555e-05
BHLHE40#8553444.87181354697742.46312701995675e-071.28238545781288e-05
BRCA1#672420.18423064322386.02116732184487e-060.000179413607396906
CCNT2#90546.336201576962630.0006203100587215640.00511685982330159
CEBPB#105147.971147625824820.0002476385788090830.0026781739186333
CTCF#1066445.360256373075030.001211145381643620.0081659659466416
E2F6#187645.017155731697390.00157802193473060.00996174037967414
EBF1#187948.9064668465690.00015887907472010.00199485112823906
EGR1#195844.988179094810140.001615011500076050.0101370386475415
ELF1#199744.258097958807540.003041525565781240.0160764152317742
ELK4#2005416.2356816584681.43847748454449e-050.000343154751046921
EP300#203346.77394172622320.0004748459821442640.00433841654528605
FOS#235348.99795530889440.0001525147711168630.00194724818834646
FOSL1#8061439.7135797163734.01511434669553e-071.93777507973445e-05
FOSL2#2355416.93020060456171.2165416097647e-050.000303232432415789
FOXA1#3169411.08141974938556.62943068949433e-050.00106962940179221
FOXA2#3170424.63046375266522.71504128667089e-069.41734297371706e-05
GABPB1#255347.067683836182170.0004006876864423170.00390040276673959
GATA1#2623413.56030814380042.95627390049268e-050.000613695666653856
GATA2#2624412.7449317335543.78864877853583e-050.000721259004341057
GTF2F1#2962412.73966087675773.79492332235515e-050.000716964538464996
HDAC2#3066413.41562023662633.0859005065161e-050.000626045771173339
HEY1#2346244.040111043105710.00375304636917980.0185809153709775
HMGN3#932448.178547723350590.0002234570284440470.00247903426743869
IRF1#365947.63716375356390.0002938853996185490.00307145974689899
IRF4#3662421.91451268674414.33289161192893e-060.000136261025913353
JUN#3725412.51282919233634.07770316866756e-050.000742194564713265
JUNB#3726430.61063265982111.13787152942193e-064.65302132581431e-05
JUND#372746.994663941871030.000417684217818580.0039126847273078
MAX#414946.452555509007120.0005767613195645490.00485073083056868
MEF2A#4205418.74323090964418.0978922767748e-060.000224333095887025
MEF2C#4208441.31135449262413.42889182145094e-071.69800869104085e-05
MXI1#460149.96157162875930.0001015224754950450.00142225430157303
MYC#460945.22228187160940.001344309395272740.00886856982710437
NANOG#79923429.24477848101271.36586687657858e-065.32672780892422e-05
NFKB1#479045.488063424193840.001102199566301980.00767417470033415
NR3C1#2908414.9730233311731.98868032687801e-050.000442376538144435
PAX5#507946.669565531177830.0005052774169483260.00443488260767007
POU2F2#545249.106124057742520.000145395665174930.00188282428706813
RAD21#5885410.35503389545638.6948481184721e-050.00129227443097354
REST#597849.650028716128020.0001152825614219170.00156852467852314
RFX5#5993412.04791082719514.74457429336527e-050.00082613970427605
RXRA#6256420.07461713913336.1537798808435e-060.000181963368339585
SIN3A#2594245.408884726815140.001168172384885160.00795376202523116
SMARCC1#6599332.74751948972364.71941722862287e-050.000824784497891807
SMC3#9126415.04493284493281.95092670935632e-050.000437331690488226
SP1#666745.69838137814090.0009482606065333980.00683568397886123
STAT1#6772420.70658749719925.43610708103893e-060.000165185216012984
STAT2#6773465.26377118644075.50053512607993e-083.46275098271646e-06
STAT3#6774410.51946499715428.16377768286615e-050.00123032724014554
TAF1#687243.343046285745290.008005664898701650.0321813493073978
TAF7#6879411.43306940492395.85061525419808e-050.000968048806294666
TAL1#6886429.86861667744021.25525650806991e-065.03447520915181e-05
TBP#690843.706770687096390.005296377814784350.0243881840570637
TCF12#6938410.63446490218647.8163066689251e-050.0011995991949976
TCF7L2#6934410.77017656313737.42969445082454e-050.00115280026556182
TFAP2C#7022410.80922860986027.32289634782688e-050.00114473278202468
THAP1#55145431.36914460285131.03171810326891e-064.31524257057676e-05
USF1#739146.361499277207960.0006105011399140830.0050752311192778
USF2#7392412.99219738506963.50833029870167e-050.000680799903504466
YY1#752844.911170749853860.00171871838055440.0106718923273913
ZEB1#6935416.88843201754391.22862303393937e-050.000303994695668311
ZNF263#1012748.221841637010680.0002187871180958320.00248530648540468



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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