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Coexpression cluster:C4388: Difference between revisions

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{{Coexpression_clusters
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.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.00084829,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.00199458,0.252796,0.205954,0.0107847|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,1.23863,1.23181,5.26168,0.820209,0.985163,1.94915,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,1.46099,2.64886,0.596053,0.855276,0.567465,2.05816,0.598234,0.777097,0.259059,0.63803,2.78317,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,2.87582,1.06461,0.396746,1.12884,1.20029,2.9247,0.459024,1.14559,0.960908,0.498519,1.39759,0.977977,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,4.5214,1.39614,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,1.33389,0.853445,0.698641,1.37083,1.21015,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.56135|tfbs_overrepresentation_jaspar=MA0003.1;1.0927,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;1.80735,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;0.904546,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.886807,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;2.99448,MA0063.1;0,MA0066.1;5.08367,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;0.211629,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;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;0.646932,MA0103.1;0.628063,MA0105.1;3.21605,MA0106.1;0.986396,MA0107.1;0.556367,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;1.3784,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;3.75836,MA0144.1;0.531867,MA0145.1;0.752137,MA0146.1;2.3244,MA0147.1;1.38767,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;1.141,MA0035.2;0.894194,MA0039.2;2.15877,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;1.2307,MA0047.2;0.973066,MA0112.2;2.88736,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;0.711948,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.455568,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;3.14419,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4388_Wilms_Neutrophils_Eosinophils_Mast_Reticulocytes_extraskeletal_CD14
|id=C4388
}}

Latest revision as of 12:44, 17 September 2013


Full id: C4388_Wilms_Neutrophils_Eosinophils_Mast_Reticulocytes_extraskeletal_CD14



Phase1 CAGE Peaks

Hg19::chr4:160024162..160024202,+p@chr4:160024162..160024202
+
Hg19::chr4:160024207..160024239,+p@chr4:160024207..160024239
+
Hg19::chr4:160024245..160024256,+p@chr4:160024245..160024256
+


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
leukocyte4.10e-23136
hematopoietic stem cell9.76e-20168
angioblastic mesenchymal cell9.76e-20168
hematopoietic lineage restricted progenitor cell2.66e-19120
classical monocyte4.47e-1842
CD14-positive, CD16-negative classical monocyte4.47e-1842
hematopoietic oligopotent progenitor cell1.73e-17161
hematopoietic multipotent progenitor cell1.73e-17161
hematopoietic cell9.93e-17177
nongranular leukocyte1.34e-16115
myeloid leukocyte2.70e-1672
defensive cell1.14e-1348
phagocyte1.14e-1348
myeloid lineage restricted progenitor cell3.06e-1366
granulocyte monocyte progenitor cell3.71e-1367
myeloid cell8.28e-12108
common myeloid progenitor8.28e-12108
macrophage dendritic cell progenitor4.85e-1161
monopoietic cell1.48e-1059
monocyte1.48e-1059
monoblast1.48e-1059
promonocyte1.48e-1059
nucleate cell7.36e-0755
Uber Anatomy
Ontology termp-valuen
adult organism2.10e-24114
neural tube5.52e-1856
neural rod5.52e-1856
future spinal cord5.52e-1856
neural keel5.52e-1856
regional part of nervous system4.45e-1753
regional part of brain4.45e-1753
central nervous system2.39e-1681
regional part of forebrain3.80e-1641
forebrain3.80e-1641
anterior neural tube3.80e-1641
future forebrain3.80e-1641
telencephalon9.41e-1534
brain grey matter1.05e-1434
gray matter1.05e-1434
nervous system1.83e-1489
cerebral hemisphere2.09e-1432
regional part of telencephalon5.28e-1432
hematopoietic system2.09e-1398
blood island2.09e-1398
regional part of cerebral cortex6.10e-1322
brain1.07e-1268
future brain1.07e-1268
cerebral cortex1.47e-1225
pallium1.47e-1225
neocortex8.78e-1220
neurectoderm1.74e-1186
neural plate2.03e-1182
presumptive neural plate2.03e-1182
hemolymphoid system4.09e-11108
bone marrow4.04e-1076
bone element6.11e-1082
pre-chordal neural plate1.24e-0961
immune system2.37e-0893
skeletal element3.23e-0790


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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.12.99448
MA0063.10
MA0066.15.08367
MA0067.11.65513
MA0068.10.405474
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
MA0088.10.257905
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
MA0105.13.21605
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.11.80901
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
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
MA0143.13.75836
MA0144.10.531867
MA0145.10.752137
MA0146.12.3244
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.22.15877
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.22.88736
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.23.14419
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
CEBPB#105137.971147625824820.001974187055288560.011558589632654
E2F1#186934.907389214879320.008460985347239390.0326856611311387
E2F6#187635.017155731697390.00791769806886330.032365903503621
EBF1#187938.9064668465690.00141523283560980.00918046597007779
EGR1#195834.988179094810140.008056488137383440.0321825039043867
ELF1#199734.258097958807540.01295179875054610.04641501937715
FOS#235338.99795530889440.001372499272417130.0090044884422371
FOSL2#2355316.93020060456170.0002060162053171620.00243753556894971
FOXA1#3169311.08141974938550.000734755275698670.00583197341835335
GABPB1#255337.067683836182170.002832212825417420.015460666698399
HMGN3#932438.178547723350590.001827766942164210.0108986669524801
IRF1#365937.63716375356390.002244692747297240.0128513028086272
JUN#3725312.51282919233630.0005103313992726250.00445565131321131
NFYA#4800318.42558069983050.0001598135507814160.00200105112457264
NFYB#4801316.75979325353650.0002123649923296180.00246462800687999
PBX3#5090321.91451268674419.49854535978121e-050.00137170710568334
SIN3A#2594235.408884726815140.006318961977991520.0277743390437884
SP1#666735.69838137814090.005403962701712170.0247471919935156
SP2#6668326.15353049384465.58768218891694e-050.00094185271163379
SPI1#668838.204323508522730.001810593189410520.0109298041794604
YY1#752834.911170749853860.008441455341808260.0330602300387412
ZBTB7A#5134137.35190930787590.002516255860282270.0140660089809998
ZEB1#6935316.88843201754390.0002075486917327580.00243443147078588
ZNF263#1012738.221841637010680.001799043925565870.0109800343935352



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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