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{{Coexpression_clusters
{
|full_id=C2430_MCF7_CD14_CD19_Natural_Neutrophils_CD8_CD4

Latest revision as of 12:05, 17 September 2013


Full id: C2430_MCF7_CD14_CD19_Natural_Neutrophils_CD8_CD4



Phase1 CAGE Peaks

Hg19::chr17:65713775..65713818,-p@chr17:65713775..65713818
-
Hg19::chr1:145507436..145507501,-p1@ENST00000421764
Hg19::chr1:149899786..149899836,+p@chr1:149899786..149899836
+
Hg19::chr9:135905830..135905859,-p@chr9:135905830..135905859
-


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
leukocyte1.36e-44136
hematopoietic stem cell7.57e-39168
angioblastic mesenchymal cell7.57e-39168
hematopoietic cell7.97e-38177
hematopoietic lineage restricted progenitor cell5.76e-37120
hematopoietic oligopotent progenitor cell1.26e-35161
hematopoietic multipotent progenitor cell1.26e-35161
nongranular leukocyte4.96e-35115
classical monocyte9.34e-2342
CD14-positive, CD16-negative classical monocyte9.34e-2342
myeloid leukocyte8.75e-2172
nucleate cell4.45e-1955
defensive cell6.62e-1948
phagocyte6.62e-1948
lymphoid lineage restricted progenitor cell7.81e-1952
lymphocyte1.56e-1853
common lymphoid progenitor1.56e-1853
myeloid cell4.70e-17108
common myeloid progenitor4.70e-17108
myeloid lineage restricted progenitor cell4.84e-1766
granulocyte monocyte progenitor cell1.83e-1667
macrophage dendritic cell progenitor8.27e-1661
monopoietic cell4.24e-1559
monocyte4.24e-1559
monoblast4.24e-1559
promonocyte4.24e-1559
native cell3.06e-14722
mature alpha-beta T cell1.66e-1018
alpha-beta T cell1.66e-1018
immature T cell1.66e-1018
mature T cell1.66e-1018
immature alpha-beta T cell1.66e-1018
T cell9.44e-1025
pro-T cell9.44e-1025
lymphocyte of B lineage1.54e-0824
pro-B cell1.54e-0824
B cell5.34e-0814
CD8-positive, alpha-beta T cell1.46e-0711
stuff accumulating cell1.49e-0787
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.00e-1998
blood island1.00e-1998
hemolymphoid system1.04e-18108
bone marrow2.18e-1476
immune system7.08e-1493
bone element1.91e-1382
skeletal element6.23e-1290
skeletal system5.39e-09100
lateral plate mesoderm9.51e-08203


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)
MA0003.10.0938548
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.11.80156
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.13.73908
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.12.17614
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.10.195821
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.23.45291
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.122011
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
BRCA1#672315.13817298241780.0004682184421431190.00430157159385866
CHD2#1106410.34402283411698.73193255208051e-050.00129044050347635
ELF1#199744.258097958807540.003041525565781240.0160853700913828
ELK4#2005312.1767612438510.0008912632577620610.00663785519342594
GABPB1#255347.067683836182170.0004006876864423170.00390222130588858
GATA1#2623310.17023110785030.001515158168498270.00966360940212465
GTF2B#2959215.97191496716210.005636585723537220.0254729284457163
GTF2F1#296239.554745657568240.001820362319304780.0108986941220977
HEY1#2346244.040111043105710.00375304636917980.018596783686045
IRF1#365947.63716375356390.0002938853996185490.00307422849066122
IRF3#3661223.49097610574480.002641101425375540.0145936189495157
NFKB1#479045.488063424193840.001102199566301980.00767775765390598
NR2C2#7182324.46095817893070.0001125906063438030.00155540348359001
POU2F2#545236.829593043306890.004860473775203740.0227592817704673
SIN3A#2594245.408884726815140.001168172384885160.00795998928068251
SIX5#147912312.81503651659420.0007664471136930380.00601585526130973
SP1#666745.69838137814090.0009482606065333980.00683898829402262
SP2#6668213.07676524692230.008330036536614940.0328071757239433
SPI1#668848.204323508522730.000220661881527680.00249439400853657
SRF#6722310.34788369662590.001439893778401260.00923716623602269
TAF1#687243.343046285745290.008005664898701650.0322073819859592
TBP#690843.706770687096390.005296377814784350.0244097084240882
TRIM28#10155313.94289378394690.0005972858184258420.00499319087413563
YY1#752844.911170749853860.00171871838055440.0106820536150155
ZBTB33#10009215.83236251499060.005734248930324640.0258382614563023



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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