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Coexpression cluster:C1964: Difference between revisions

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{{Coexpression_clusters
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|full_id=C1964_Mast_Hepatocyte_CD14_granulocyte_liver_Macrophage_acute
|id=C1964
}}

Latest revision as of 11:56, 17 September 2013


Full id: C1964_Mast_Hepatocyte_CD14_granulocyte_liver_Macrophage_acute



Phase1 CAGE Peaks

Hg19::chr5:75699040..75699090,+p3@IQGAP2
Hg19::chr5:75699091..75699117,+p1@IQGAP2
Hg19::chr5:75699125..75699136,+p7@IQGAP2
Hg19::chr5:75699154..75699180,+p2@IQGAP2
Hg19::chr5:75699195..75699206,+p6@IQGAP2


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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell6.52e-54168
angioblastic mesenchymal cell6.52e-54168
hematopoietic oligopotent progenitor cell1.31e-50161
hematopoietic multipotent progenitor cell1.31e-50161
hematopoietic cell6.90e-50177
leukocyte2.28e-43136
hematopoietic lineage restricted progenitor cell4.66e-38120
nongranular leukocyte4.66e-36115
myeloid cell2.31e-35108
common myeloid progenitor2.31e-35108
myeloid leukocyte7.64e-2772
granulocyte monocyte progenitor cell3.72e-2567
myeloid lineage restricted progenitor cell7.88e-2566
macrophage dendritic cell progenitor4.39e-2161
monopoietic cell5.36e-2159
monocyte5.36e-2159
monoblast5.36e-2159
promonocyte5.36e-2159
defensive cell6.84e-2148
phagocyte6.84e-2148
classical monocyte1.09e-1742
CD14-positive, CD16-negative classical monocyte1.09e-1742
nucleate cell1.04e-1355
lymphocyte2.93e-1353
common lymphoid progenitor2.93e-1353
lymphoid lineage restricted progenitor cell6.58e-1352
T cell3.46e-1025
pro-T cell3.46e-1025
mature alpha-beta T cell5.15e-1018
alpha-beta T cell5.15e-1018
immature T cell5.15e-1018
mature T cell5.15e-1018
immature alpha-beta T cell5.15e-1018
stuff accumulating cell3.78e-0787
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.08e-2998
blood island6.08e-2998
hemolymphoid system3.54e-25108
bone marrow2.17e-2076
immune system4.05e-1993
bone element9.14e-1982
skeletal element1.76e-1490
adult organism8.63e-12114
skeletal system5.26e-11100
blood1.91e-0715
haemolymphatic fluid1.91e-0715
organism substance1.91e-0715
Disease
Ontology termp-valuen
leukemia1.25e-0839
myeloid leukemia2.96e-0731
hematologic cancer2.99e-0751
immune system cancer2.99e-0751


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)
MA0003.10.481059
MA0004.10.626788
MA0006.12.97829
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.14.94778
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.603517
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.11.29682
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.692739
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0140295
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.3271
MA0089.10
MA0090.10.556637
MA0091.15.03975
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.520776
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.12.96863
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.11.87149
MA0144.10.356507
MA0145.10.442008
MA0146.10.6031
MA0147.13.65004
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.527987
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.25.26066
MA0047.20.767096
MA0112.21.96224
MA0065.23.49428
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.15.57055
MA0155.16.71259
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.13.1409
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.23.54347
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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#90556.336201576962639.78880505817628e-050.00139168664779591
CTCF#1066455.360256373075030.0002259278299937090.00250219264440222
CTCFL#140690519.74647435897443.32745051287657e-071.65957786109989e-05
E2F6#187655.017155731697390.0003144978599297790.00323190416148836
EBF1#187958.9064668465691.78355672307702e-050.000406709346291356
EGR1#195854.988179094810140.0003237398000590710.00331091470606829
ELF1#199754.258097958807540.0007142416939776840.00573761158967275
EP300#203356.77394172622327.00901578206049e-050.00110995390335499
ETS1#211359.728760922202341.14685159850452e-050.000292350583588512
GABPB1#255357.067683836182175.6685482528729e-050.000949506833972402
GATA1#2623513.56030814380042.17950082879909e-067.83832255712631e-05
GATA2#2624512.7449317335542.9719152914525e-060.000101300215771543
HDAC2#3066513.41562023662632.29961139448262e-068.18572305481836e-05
HEY1#2346254.040111043105710.0009288852205177990.00674864998578493
HMGN3#932458.178547723350592.73180911341838e-050.000582854774251894
JUND#372756.994663941871035.97069468343598e-050.000985263678374735
MAX#414956.452555509007128.93743970843928e-050.0013076733898987
MYC#460955.22228187160940.0002573944848850610.00276734842566511
NFKB1#479055.488063424193840.0002008162847462320.00239336436866503
PAX5#507956.669565531177837.57493746384605e-050.0011715073208746
RAD21#5885510.35503389545638.39503550283973e-060.000229942069992415
SMC3#9126515.04493284493281.29633924985553e-065.16946830529445e-05
SP1#666755.69838137814090.000166391843712550.00204516862015947
SPI1#668858.204323508522732.68916109982495e-050.000575519049394709
TAF1#687253.343046285745290.002394600090870310.0135549939777997
TBP#690853.706770687096390.001428755106721120.00920245171698102
TCF12#6938510.63446490218647.34844389925727e-060.000211480885201028
USF1#739156.361499277207969.59569864925045e-050.00137057600003975
USF2#7392512.99219738506962.69963551658264e-069.4359850641357e-05
YY1#752854.911170749853860.00034993140821360.00353140268068607
ZBTB7A#5134157.35190930787594.65425347594289e-050.00081653885229968
ZEB1#6935516.88843201754397.27243686732534e-073.23753637675444e-05
ZNF143#7702513.50087655222792.22790360787208e-067.97942472230973e-05



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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