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Coexpression cluster:C4171: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.178364,MA0004.1;3.20493,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;2.78037,MA0041.1;1.97353,MA0042.1;0.810843,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;5.50871,MA0059.1;5.50056,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;2.86846,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;5.11284,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;1.66081,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;2.18164,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;2.37462,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;2.13189,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;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;2.02335,MA0161.1;0,MA0162.1;0.8915,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;1.55139,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.00160703,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;1.40979,MA0442.1;0
}}
}}

Revision as of 21:52, 22 January 2013


Full id: C4171_CD14_meningioma_Endothelial_adult_immature_mesothelioma_b



Phase1 CAGE Peaks

Hg19::chr2:201994042..201994070,+p10@CFLAR
Hg19::chr2:201994073..201994085,+p21@CFLAR
Hg19::chr2:201994091..201994109,+p20@CFLAR


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
classical monocyte2.97e-1842
CD14-positive, CD16-negative classical monocyte2.97e-1842
defensive cell1.97e-1748
phagocyte1.97e-1748
endothelial cell of vascular tree2.86e-1624
macrophage dendritic cell progenitor2.61e-1361
blood vessel endothelial cell1.13e-1218
embryonic blood vessel endothelial progenitor cell1.13e-1218
monopoietic cell3.74e-1259
monocyte3.74e-1259
monoblast3.74e-1259
promonocyte3.74e-1259
granulocyte monocyte progenitor cell9.76e-1267
endothelial cell1.75e-1136
lining cell1.97e-1158
barrier cell1.97e-1158
meso-epithelial cell8.59e-1145
myeloid lineage restricted progenitor cell3.00e-1066
myeloid leukocyte7.28e-1072
hematopoietic lineage restricted progenitor cell1.82e-09120
nongranular leukocyte3.20e-09115
leukocyte9.35e-09136
mesodermal cell2.48e-08121
endothelial cell of artery1.33e-079
myeloid cell2.53e-07108
common myeloid progenitor2.53e-07108
hematopoietic oligopotent progenitor cell2.69e-07161
hematopoietic multipotent progenitor cell2.69e-07161
Uber Anatomy
Ontology termp-valuen
vessel2.97e-1668
lateral plate mesoderm3.20e-16203
epithelial tube open at both ends7.47e-1459
blood vessel7.47e-1459
blood vasculature7.47e-1459
vascular cord7.47e-1459
blood vessel endothelium1.13e-1218
endothelium1.13e-1218
cardiovascular system endothelium1.13e-1218
splanchnic layer of lateral plate mesoderm6.03e-1283
immune system9.41e-1293
vasculature1.49e-1178
vascular system1.49e-1178
artery2.17e-1142
arterial blood vessel2.17e-1142
arterial system2.17e-1142
simple squamous epithelium4.38e-1122
circulatory system1.33e-10112
hemolymphoid system2.16e-10108
epithelial tube7.13e-10117
cardiovascular system1.04e-09109
systemic artery2.93e-0933
systemic arterial system2.93e-0933
squamous epithelium1.19e-0825
bone marrow2.77e-0876
mesoderm3.05e-08315
mesoderm-derived structure3.05e-08315
presumptive mesoderm3.05e-08315
hematopoietic system5.04e-0898
blood island5.04e-0898
endothelial tube1.33e-079
arterial system endothelium1.33e-079
endothelium of artery1.33e-079


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
MA0004.13.20493
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
MA0040.12.78037
MA0041.11.97353
MA0042.10.810843
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
MA0058.15.50871
MA0059.15.50056
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
MA0077.12.86846
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
MA0093.15.11284
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
MA0119.11.66081
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.12.18164
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.12.37462
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
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
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.12.02335
MA0161.10
MA0162.10.8915
MA0163.10.122425
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.20.00160703
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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-050.0011005636971856
BCL11A#53335328.36945510360714.37778126761649e-050.00077849667598944
EGR1#195834.988179094810140.008056488137383440.0321345693774897
ELF1#199734.258097958807540.01295179875054610.0463450477852566
EP300#203336.77394172622320.003216880500103790.0167790931703711
FOS#235338.99795530889440.001372499272417130.0089931897554409
FOXA1#3169311.08141974938550.000734755275698670.00582400624155232
FOXA2#3170324.63046375266526.68983856509345e-050.00107373605332687
IRF4#3662321.91451268674419.49854535978121e-050.0013692457954868
MAX#414936.452555509007120.003721913834265510.018696212733243
NFKB1#479035.488063424193840.006049381815655430.0270123300459719
NR3C1#2908314.9730233311730.0002978331194675480.00309414037243323
SPI1#668838.204323508522730.001810593189410520.0109234903881258
SRF#6722313.79717826216780.0003806615025800190.00375693693705865
STAT3#6774310.51946499715420.0008589184530415310.00643735804213882
TCF7L2#6934310.77017656313730.0008003181298398380.00615088859830325
USF1#739136.361499277207960.00388404057290560.0190748289943425
USF2#7392312.99219738506960.0004558979393427810.00422292903654286



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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