Personal tools

Coexpression cluster:C2856: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
Line 1: Line 1:
{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 12:14, 17 September 2013


Full id: C2856_Mast_Neutrophils_Eosinophils_CD14_CD133_CD34_immature



Phase1 CAGE Peaks

Hg19::chr6:31702520..31702537,-p@chr6:31702520..31702537
-
Hg19::chr6:31705781..31705817,-p@chr6:31705781..31705817
-
Hg19::chr6:31705825..31705837,-p@chr6:31705825..31705837
-
Hg19::chr6:31705970..31706014,+p@chr6:31705970..31706014
+


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 cell4.19e-55177
hematopoietic stem cell4.33e-53168
angioblastic mesenchymal cell4.33e-53168
hematopoietic oligopotent progenitor cell1.06e-49161
hematopoietic multipotent progenitor cell1.06e-49161
myeloid cell8.13e-48108
common myeloid progenitor8.13e-48108
leukocyte3.48e-40136
myeloid leukocyte1.10e-3772
hematopoietic lineage restricted progenitor cell3.07e-34120
myeloid lineage restricted progenitor cell1.20e-3166
classical monocyte1.23e-3142
CD14-positive, CD16-negative classical monocyte1.23e-3142
granulocyte monocyte progenitor cell1.59e-3167
nongranular leukocyte8.14e-30115
defensive cell7.46e-2948
phagocyte7.46e-2948
macrophage dendritic cell progenitor2.81e-2861
monopoietic cell5.38e-2759
monocyte5.38e-2759
monoblast5.38e-2759
promonocyte5.38e-2759
mesenchymal cell8.40e-19354
connective tissue cell1.09e-18361
motile cell1.61e-15386
multi fate stem cell1.00e-13427
stem cell1.94e-13441
somatic stem cell9.89e-13433
stuff accumulating cell1.77e-1087
somatic cell2.10e-08588
granulocyte5.06e-088
intermediate monocyte1.45e-079
CD14-positive, CD16-positive monocyte1.45e-079
blood cell1.83e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.71e-3698
blood island1.71e-3698
hemolymphoid system2.36e-33108
bone marrow2.03e-2876
immune system4.31e-2793
bone element4.23e-2682
skeletal element1.38e-2290
skeletal system1.83e-20100
connective tissue1.09e-17371
lateral plate mesoderm1.69e-17203
musculoskeletal system3.33e-09167
blood4.43e-0715
haemolymphatic fluid4.43e-0715
organism substance4.43e-0715
Disease
Ontology termp-valuen
leukemia6.44e-1339
myeloid leukemia9.40e-1331
hematologic cancer7.25e-1251
immune system cancer7.25e-1251


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
MA0007.11.65296
MA0009.12.70386
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
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
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.11.68681
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.11.8408
MA0072.11.1744
MA0073.11.53734
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.12.50276
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
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
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.21.75253
MA0137.21.37305
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.14.10107
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.0725493
MA0164.10.90014
MA0080.21.32578
MA0018.22.02192
MA0099.20.7872
MA0079.20.476674
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
BCL11A#53335428.36945510360711.542446414682e-065.90511587620871e-05
E2F6#187645.017155731697390.00157802193473060.00999012140639686
ELF1#199744.258097958807540.003041525565781240.016122926026019
EP300#203346.77394172622320.0004748459821442640.00435174092042513
GTF2F1#296239.554745657568240.001820362319304780.010904320061134
HDAC2#3066413.41562023662633.0859005065161e-050.000628364911288818
HEY1#2346244.040111043105710.00375304636917980.0186560880414455
JUN#3725412.51282919233634.07770316866756e-050.000744920834760314
JUND#372746.994663941871030.000417684217818580.00392500648054298
NFKB1#479045.488063424193840.001102199566301980.00769160901409944
PAX5#507935.002174148383370.01196533174786410.0435235191702137
POU2F2#545249.106124057742520.000145395665174930.00188750501867054
SIN3A#2594245.408884726815140.001168172384885160.00797925151765996
SMARCA4#65974156.7659033078881.64738581138188e-091.44702545630708e-07
SP1#666745.69838137814090.0009482606065333980.00685650716461794
SPI1#668848.204323508522730.000220661881527680.00249845037346806
SRF#6722310.34788369662590.001439893778401260.0092422756021418
STAT2#6773348.94782838983051.42094046481278e-050.000340683198357626
TBP#690843.706770687096390.005296377814784350.0244972720371241
YY1#752844.911170749853860.00171871838055440.0107043490337361



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C2856&oldid=3069973"