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Coexpression cluster:C4802: Difference between revisions

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{{Coexpression_clusters
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.158479,0.220319,0.195218,0.124213,0.259632,0.0532009,0.180606,0.159884,0.00351525,0.150733,0.217112,0.123917,0.184317,0.0183464,0.0723291,0.258496,0.261744,0.0223377,0.21382,0.0232077,0.141867,0.0199603,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.0129343,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.00312563,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.0297055,0.189559,0.00339727,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.00954842,0.0224775,0.0488311,0.0457063,0.00940743,0.141729,0.0037817,0.255956,0.0215087,0.227491,0.29837,0.253509,0.177664,0.00482769,0.264413,0.00908908,0.000785583,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.0257187,0.223831,0.00691586,0.194982,0.190993,0.281727,0.0445413,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.0133429,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,5.1311,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,1.84557,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,2.2774,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,1.85641,0.842925,1.55576,0.388328,0.795576,1.21459,0.534793,0.439574,1.46099,9.86358,0.596053,0.855276,0.567465,2.05816,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,1.60305,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.82001,3.62511,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,2.12604,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,2.54931,2.14531,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.974093,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,2.3415,0.698641,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,2.85375,1.11698,0.960047,2.24188,0.936473,0.56135|tfbs_overrepresentation_jaspar=MA0003.1;1.54338,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;1.24048,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;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;1.62115,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.557638,MA0056.1;0,MA0057.1;7.64787,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;1.04561,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.211629,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;5.67475,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;0.767139,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;1.12079,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;1.37817,MA0146.1;0.348055,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.195278,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;3.77966,MA0065.2;2.13692,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.838867,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;2.02335,MA0161.1;0,MA0162.1;0.455568,MA0163.1;0.776149,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;18.6494,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4802_Mast_Neutrophils_Eosinophils_Natural_CD14_Basophils_CD8
|id=C4802
|ontology_enrichment_celltype=CL:0002057!6.86e-24!42;CL:0000860!1.89e-23!45;CL:0000766!5.39e-22!76;CL:0000557!5.12e-18!71;CL:0000839!8.81e-16!70;CL:0002009!1.24e-15!65;CL:0002194!2.12e-15!63;CL:0000576!2.12e-15!63;CL:0000040!2.12e-15!63;CL:0000559!2.12e-15!63;CL:0000763!2.53e-11!112;CL:0000049!2.53e-11!112;CL:0000738!1.28e-10!140;CL:0002031!4.71e-07!124;CL:0000094!9.94e-07!8
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.94e-19!102;UBERON:0003061!1.94e-19!102;UBERON:0002193!5.38e-16!112;UBERON:0002371!1.18e-15!80;UBERON:0001474!2.37e-15!86;UBERON:0003081!2.64e-14!216;UBERON:0004765!2.26e-10!101;UBERON:0001434!2.26e-10!101;UBERON:0002405!1.70e-08!115
}}

Latest revision as of 14:20, 17 September 2013


Full id: C4802_Mast_Neutrophils_Eosinophils_Natural_CD14_Basophils_CD8



Phase1 CAGE Peaks

Hg19::chr9:132222772..132222790,+p@chr9:132222772..132222790
+
Hg19::chr9:132222825..132222843,+p@chr9:132222825..132222843
+
Hg19::chr9:132222848..132222877,+p@chr9:132222848..132222877
+


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>

Uber Anatomy
Ontology termp-valuen
hematopoietic system5.04e-1898
blood island5.04e-1898
bone marrow2.99e-1576
hemolymphoid system3.88e-15108
bone element8.39e-1582
lateral plate mesoderm5.96e-13203
skeletal element7.97e-1390
immune system6.28e-1293
skeletal system4.39e-10100


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)
MA0003.11.54338
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
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
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.17.64787
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.211629
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.15.67475
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
MA0111.10.767139
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
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.11.37817
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.23.77966
MA0065.22.13692
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.12.02335
MA0161.10
MA0162.10.455568
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.218.6494
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
CCNT2#90536.336201576962630.003930750035764890.0191386295098018
CEBPB#105137.971147625824820.001974187055288560.0115878222822054
CTCF#1066435.360256373075030.0064925092527670.0281672900697767
CTCFL#140690319.74647435897440.0001298372005551160.00172454119150144
E2F1#186934.907389214879320.008460985347239390.0328143209432335
E2F4#1874312.66806031528440.0004917987006298980.00439375230924602
E2F6#187635.017155731697390.00791769806886330.0324739423740973
EGR1#195834.988179094810140.008056488137383440.0322837572259598
ELF1#199734.258097958807540.01295179875054610.0465331765698264
EP300#203336.77394172622320.003216880500103790.0168616202032793
ESR1#2099330.76860329615453.43136389821584e-050.000679886575916835
ETS1#211339.728760922202340.001085840092584840.00765933090837956
FOS#235338.99795530889440.001372499272417130.00902489778454779
FOSL1#8061339.7135797163731.59554825631833e-050.000372957619385923
FOSL2#2355316.93020060456170.0002060162053171620.00244140774618394
FOXA1#3169311.08141974938550.000734755275698670.00584797334542702
FOXA2#3170324.63046375266526.68983856509345e-050.00107771101326515
GABPB1#255337.067683836182170.002832212825417420.015493058625276
HDAC2#3066313.41562023662630.0004140761399857210.00393966456991607
HMGN3#932438.178547723350590.001827766942164210.0109342508690966
HNF4A#3172323.13229036295378.07584663437677e-050.00123543774226992
HNF4G#3174328.75342252644684.20470658818262e-050.0007611983902985
JUND#372736.994663941871030.002921845042734990.0157792323500801
MXI1#460139.96157162875930.001011470541259020.00723937581267482
MYC#460935.22228187160940.007020843755740150.0296418280715425
NANOG#79923329.24477848101273.99627955670032e-050.000741986561106178
PAX5#507936.669565531177830.003370290999677260.0173779225729595
RAD21#5885310.35503389545630.0009004912073565420.00669274133255834
REST#597839.650028716128020.001112636247114590.00772007819641248
RXRA#6256320.07461713913330.0001235730348432220.00166119760406633
SIN3A#2594235.408884726815140.006318961977991520.0278575799923789
SMC3#9126315.04493284493280.0002935825420371870.00311031315762038
SP1#666735.69838137814090.005403962701712170.0248113799887509
SPI1#668838.204323508522730.001810593189410520.0109475216875381
SREBF1#6720347.00584944048839.62099323994382e-060.000255481035592803
TAF7#6879311.43306940492390.0006690181981945830.00546213192630113
TCF12#6938310.63446490218640.0008313523990202070.0063247095863397
TCF7L2#6934310.77017656313730.0008003181298398380.00617953756929934
USF1#739136.361499277207960.00388404057290560.0191351154957162
YY1#752834.911170749853860.008441455341808260.0331522263168169
ZBTB7A#5134137.35190930787590.002516255860282270.0141082968697063
ZNF263#1012738.221841637010680.001799043925565870.0110231943996582



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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