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Coexpression cluster:C4502: Difference between revisions

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{{Coexpression_clusters
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913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,1.23181,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,1.60265,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,2.27558,0.439574,1.46099,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.718382,0.63803,0.151453,1.72524,0.939121,0.808003,1.28131,0.645308,1.02504,0.951993,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,1.10051,0.414196,0.396746,2.54768,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.82001,0.381882,1.053,2.0169,3.57435,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,2.12604,0.743661,2.55998,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,2.54931,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,2.29164,0.853445,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232|tfbs_overrepresentation_jaspar=MA0003.1;0.0471418,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;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;0.190716,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;0.715722,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;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.752137,MA0146.1;1.16674,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.0526989,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;2.70092,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.731309,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;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;1.55139,MA0018.2;0.987913,MA0099.2;2.08754,MA0079.2;0.00160703,MA0102.2;1.88331,MA0258.1;2.22591,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4502_CD14_large_alveolar_embryonic_clear_acute_bronchogenic
|id=C4502
}}

Latest revision as of 14:14, 17 September 2013


Full id: C4502_CD14_large_alveolar_embryonic_clear_acute_bronchogenic



Phase1 CAGE Peaks

Hg19::chr5:42993321..42993352,-p2@uc003jnb.1
Hg19::chr5:42993353..42993378,-p3@uc003jnb.1
Hg19::chr5:42993398..42993411,-p5@uc003jnb.1


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 leukocyte4.80e-2472
classical monocyte6.93e-2242
CD14-positive, CD16-negative classical monocyte6.93e-2242
defensive cell2.37e-2148
phagocyte2.37e-2148
connective tissue cell6.66e-20361
granulocyte monocyte progenitor cell9.65e-2067
monopoietic cell3.72e-1959
monocyte3.72e-1959
monoblast3.72e-1959
promonocyte3.72e-1959
multi fate stem cell6.18e-19427
mesenchymal cell8.30e-19354
leukocyte9.17e-19136
myeloid lineage restricted progenitor cell1.26e-1866
macrophage dendritic cell progenitor1.29e-1861
somatic stem cell1.27e-17433
stem cell1.92e-17441
nongranular leukocyte1.24e-16115
hematopoietic stem cell2.26e-16168
angioblastic mesenchymal cell2.26e-16168
myeloid cell2.92e-16108
common myeloid progenitor2.92e-16108
hematopoietic cell3.50e-16177
hematopoietic lineage restricted progenitor cell4.56e-16120
hematopoietic oligopotent progenitor cell1.00e-15161
hematopoietic multipotent progenitor cell1.00e-15161
somatic cell3.94e-15588
motile cell1.96e-13386
endothelial cell7.95e-1236
endothelial cell of vascular tree1.42e-1024
native cell4.30e-10722
stuff accumulating cell4.09e-0987
meso-epithelial cell7.11e-0945
blood vessel endothelial cell4.84e-0818
embryonic blood vessel endothelial progenitor cell4.84e-0818
Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.73e-26108
hematopoietic system3.69e-2398
blood island3.69e-2398
immune system8.17e-2393
bone marrow2.64e-2076
skeletal element3.49e-2090
skeletal system1.45e-19100
bone element1.51e-1982
connective tissue7.20e-19371
lateral plate mesoderm2.14e-18203
mesoderm2.39e-15315
mesoderm-derived structure2.39e-15315
presumptive mesoderm2.39e-15315
musculoskeletal system2.91e-14167
blood vessel endothelium4.84e-0818
endothelium4.84e-0818
cardiovascular system endothelium4.84e-0818
cardiovascular system1.35e-07109
circulatory system3.67e-07112
simple squamous epithelium9.66e-0722


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)
MA0003.10.0471418
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
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
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
MA0088.10.715722
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.22.70092
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
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
MA0080.21.55139
MA0018.20.987913
MA0099.22.08754
MA0079.20.00160703
MA0102.21.88331
MA0258.12.22591
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-050.00110190666691981
BCLAF1#9774214.43509840674790.006201147435546130.0273983262975295
BRCA1#672320.18423064322380.0001215704860271640.00164443724779056
CEBPB#105137.971147625824820.001974187055288560.0115631272428513
CTCF#1066435.360256373075030.0064925092527670.0280926036313433
ELF1#199734.258097958807540.01295179875054610.046446894540682
ELK4#2005316.2356816584680.0002336043955745990.00256248392704711
EP300#203336.77394172622320.003216880500103790.0168152043318488
FOS#235338.99795530889440.001372499272417130.00900844969280873
FOSL1#8061339.7135797163731.59554825631833e-050.000372207872105495
FOSL2#2355316.93020060456170.0002060162053171620.00243891707856711
GABPB1#255337.067683836182170.002832212825417420.0154695609682428
GTF2B#2959331.94382993432423.06634405746243e-050.000629290444129139
GTF2F1#2962312.73966087675770.0004835525047438590.00435510003819799
IRF4#3662321.91451268674419.49854535978121e-050.00137246621310209
JUN#3725312.51282919233630.0005103313992726250.00445863317790143
JUNB#3726330.61063265982113.4847716247536e-050.000681930042566314
JUND#372736.994663941871030.002921845042734990.0157434130123407
MAX#414936.452555509007120.003721913834265510.0187250329465222
MXI1#460139.96157162875930.001011470541259020.00722501688383496
MYC#460935.22228187160940.007020843755740150.0295701052952271
NFKB1#479035.488063424193840.006049381815655430.0270609237780116
NR3C1#2908314.9730233311730.0002978331194675480.00309814672948917
RAD21#5885310.35503389545630.0009004912073565420.00667421767121637
RFX5#5993312.04791082719510.0005717246050312580.00486201009892188
SMARCB1#6598318.25271578115740.000164397760679890.00203768546494743
SMARCC1#6599343.66335931963151.20046018043203e-050.000302545513475243
SMC3#9126315.04493284493280.0002935825420371870.00310401570235085
STAT1#6772320.70658749719920.0001125992441046670.00155305764065601
STAT3#6774310.51946499715420.0008589184530415310.0064484641159661
TFAP2C#7022310.80922860986020.0007916746575753130.00618227228671363
USF1#739136.361499277207960.00388404057290560.0190972794780702
USF2#7392312.99219738506960.0004558979393427810.00422667775295346



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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