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Coexpression cluster:C3952: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.718382,1.54087,0.461452,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,2.51002,1.54311,1.91674,1.2037,1.75271,0.762094,2.16826,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,1.24629,1.39759,0.169933,0.303648,0.993996,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,2.74478,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,1.44883,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,1.96632,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,1.3017,0.936473,0.0768232
|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.718382,1.54087,0.461452,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,2.51002,1.54311,1.91674,1.2037,1.75271,0.762094,2.16826,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,1.24629,1.39759,0.169933,0.303648,0.993996,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,2.74478,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,1.44883,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,1.96632,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,1.3017,0.936473,0.0768232
|tfbs_overrepresentation_jaspar=MA0003.1;0.178364,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.118426,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,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;1.97353,MA0042.1;1.89908,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;2.01615,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;0.407479,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;3.83913,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;2.34614,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;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;1.141,MA0035.2;0.894194,MA0039.2;0.0526989,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;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.256269,MA0156.1;1.60572,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;1.55139,MA0018.2;0.987913,MA0099.2;2.08754,MA0079.2;0.00160703,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 21:43, 22 January 2013


Full id: C3952_CD14_Eosinophils_cord_Mast_Basophils_Dendritic_Neutrophils



Phase1 CAGE Peaks

Hg19::chr1:234743771..234743791,-p10@IRF2BP2
Hg19::chr1:234743812..234743846,-p3@IRF2BP2
Hg19::chr1:234743854..234743870,-p11@IRF2BP2


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
myeloid leukocyte6.94e-2572
granulocyte monocyte progenitor cell1.61e-2167
myeloid cell1.04e-20108
common myeloid progenitor1.04e-20108
myeloid lineage restricted progenitor cell1.50e-2066
classical monocyte8.08e-2042
CD14-positive, CD16-negative classical monocyte8.08e-2042
macrophage dendritic cell progenitor2.39e-1861
defensive cell2.52e-1848
phagocyte2.52e-1848
leukocyte1.42e-17136
monopoietic cell2.58e-1759
monocyte2.58e-1759
monoblast2.58e-1759
promonocyte2.58e-1759
hematopoietic stem cell7.26e-16168
angioblastic mesenchymal cell7.26e-16168
hematopoietic cell7.88e-16177
hematopoietic oligopotent progenitor cell1.42e-14161
hematopoietic multipotent progenitor cell1.42e-14161
hematopoietic lineage restricted progenitor cell2.58e-13120
stuff accumulating cell3.19e-1187
nongranular leukocyte9.78e-11115
Uber Anatomy
Ontology termp-valuen
bone marrow2.60e-1976
immune system5.64e-1993
skeletal element1.95e-1790
hemolymphoid system4.30e-17108
hematopoietic system1.17e-1698
blood island1.17e-1698
bone element4.87e-1682
skeletal system4.20e-15100
lateral plate mesoderm2.00e-11203
musculoskeletal system1.46e-09167
mesoderm7.93e-07315
mesoderm-derived structure7.93e-07315
presumptive mesoderm7.93e-07315


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
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.11.97353
MA0042.11.89908
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
MA0061.12.01615
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.407479
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
MA0101.13.83913
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.12.34614
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
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.22.08754
MA0079.20.00160703
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
BATF#10538324.35780179230366.91705216281876e-050.00109955861618361
BHLHE40#8553344.87181354697741.10603738662898e-050.000284656083346831
CCNT2#90536.336201576962630.003930750035764890.0190171678781326
CEBPB#105137.971147625824820.001974187055288560.0115269258046224
CTCF#1066435.360256373075030.0064925092527670.0279663108904452
E2F6#187635.017155731697390.00791769806886330.0322497745257211
EBF1#187938.9064668465690.00141523283560980.00915714652860742
ELF1#199734.258097958807540.01295179875054610.0462657902557815
EP300#203336.77394172622320.003216880500103790.0167598414920852
FOS#235338.99795530889440.001372499272417130.00898079390464085
FOSL1#8061339.7135797163731.59554825631833e-050.000371295597909158
FOSL2#2355316.93020060456170.0002060162053171620.00243175027883353
FOXA1#3169311.08141974938550.000734755275698670.0058169425590277
FOXA2#3170324.63046375266526.68983856509345e-050.00107258220739913
GATA1#2623313.56030814380040.0004009615963782630.00388100353699253
GATA2#2624312.7449317335540.0004829527704283790.00437080627303029
GTF2B#2959331.94382993432423.06634405746243e-050.000628056299308333
GTF2F1#2962312.73966087675770.0004835525047438590.00434236801745003
HDAC2#3066313.41562023662630.0004140761399857210.00391434630557284
IRF4#3662321.91451268674419.49854535978121e-050.00136717003697656
JUN#3725312.51282919233630.0005103313992726250.00444487540727493
JUNB#3726330.61063265982113.4847716247536e-050.000680782012191623
JUND#372736.994663941871030.002921845042734990.0156883746037839
MAFF#23764356.31535648994525.59409009993116e-060.000169100195643042
MAFK#7975327.10073313782995.02195559325033e-050.000858128305306727
MAX#414936.452555509007120.003721913834265510.0186692742393187
MXI1#460139.96157162875930.001011470541259020.00720677935997755
MYC#460935.22228187160940.007020843755740150.0294738283224434
NFKB1#479035.488063424193840.006049381815655430.0269765750403603
NR3C1#2908314.9730233311730.0002978331194675480.00309137280501603
PAX5#507936.669565531177830.003370290999677260.0173027489414193
POU2F2#545239.106124057742520.001324165192682130.00882768342643489
RAD21#5885310.35503389545630.0009004912073565420.00664497994807531
REST#597839.650028716128020.001112636247114590.00768129409124806
RFX5#5993312.04791082719510.0005717246050312580.00484937432184354
RXRA#6256320.07461713913330.0001235730348432220.00165332362105961
SIN3A#2594235.408884726815140.006318961977991520.0277020555773604
SIRT6#515483153.6384039900252.75057764221434e-071.39857633094072e-05
SMARCB1#6598318.25271578115740.000164397760679890.00203213844569145
SMC3#9126315.04493284493280.0002935825420371870.00309305630059737
SPI1#668838.204323508522730.001810593189410520.0109121439268766
STAT3#6774310.51946499715420.0008589184530415310.00643043615177093
TFAP2A#7020316.5186343730450.0002218033880766340.0024833752194828
TFAP2C#7022310.80922860986020.0007916746575753130.00616154032062807
TRIM28#10155318.59052504526250.0001555969297255280.00197165587765159
USF1#739136.361499277207960.00388404057290560.0190416989810678
USF2#7392312.99219738506960.0004558979393427810.00421843934500051
WRNIP1#568973109.8199643493767.53682839543883e-073.32547030330053e-05
YY1#752834.911170749853860.008441455341808260.032967510075653



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3952&oldid=2572463"