Personal tools

Coexpression cluster:C2203

From FANTOM5_SSTAR

Jump to: navigation, search


Full id: C2203_non_Neutrophils_Eosinophils_lymphoma_CD19_Whole_Burkitt



Phase1 CAGE Peaks

  Short description
Hg19::chr12:25205628..25205657,+ p2@LRMP
Hg19::chr12:25205666..25205690,+ p4@LRMP
Hg19::chr13:28712383..28712394,+ p9@PAN3
Hg19::chr9:130540962..130540988,- p4@SH2D3C


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0006906vesicle fusion0.0195980326925824
GO:0007516hemocyte development0.0195980326925824
GO:0042386hemocyte differentiation0.0195980326925824
GO:0006903vesicle targeting0.0195980326925824
GO:0051650establishment of vesicle localization0.0195980326925824
GO:0051648vesicle localization0.0195980326925824
GO:0000184mRNA catabolic process, nonsense-mediated decay0.0281630495993967
GO:0051656establishment of organelle localization0.0281630495993967
GO:0006402mRNA catabolic process0.0315588082218239
GO:0051640organelle localization0.0323167659584715
GO:0006944membrane fusion0.032936074582253
GO:0006401RNA catabolic process0.0368945357790832
GO:0005070SH3/SH2 adaptor activity0.0368945357790832
GO:0060090molecular adaptor activity0.0415771974545133
GO:0007254JNK cascade0.0415771974545133
GO:0031098stress-activated protein kinase signaling pathway0.0415771974545133



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Cell Type
Ontology termp-valuen
hematopoietic stem cell4.21e-89168
angioblastic mesenchymal cell4.21e-89168
hematopoietic oligopotent progenitor cell2.22e-83161
hematopoietic multipotent progenitor cell2.22e-83161
hematopoietic cell7.97e-83177
leukocyte7.63e-74136
hematopoietic lineage restricted progenitor cell2.81e-60120
nongranular leukocyte6.86e-59115
myeloid cell7.92e-57108
common myeloid progenitor7.92e-57108
myeloid leukocyte6.29e-4372
granulocyte monocyte progenitor cell1.19e-3767
myeloid lineage restricted progenitor cell1.14e-3666
macrophage dendritic cell progenitor3.61e-3461
monopoietic cell1.76e-3359
monocyte1.76e-3359
monoblast1.76e-3359
promonocyte1.76e-3359
defensive cell1.97e-3048
phagocyte1.97e-3048
classical monocyte6.40e-3042
CD14-positive, CD16-negative classical monocyte6.40e-3042
nucleate cell2.30e-2255
lymphocyte7.41e-2253
common lymphoid progenitor7.41e-2253
lymphoid lineage restricted progenitor cell3.87e-2152
lymphocyte of B lineage6.79e-1924
pro-B cell6.79e-1924
mesenchymal cell1.81e-13354
connective tissue cell2.81e-12361
B cell4.23e-1214
stuff accumulating cell6.45e-0987
motile cell1.48e-08386
intermediate monocyte1.59e-089
CD14-positive, CD16-positive monocyte1.59e-089
granulocyte5.68e-088
dendritic cell9.48e-0710
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.12e-4398
blood island1.12e-4398
hemolymphoid system1.41e-40108
bone marrow1.01e-3276
immune system5.00e-3293
bone element7.16e-2982
skeletal element9.26e-2490
adult organism8.04e-21114
skeletal system2.19e-19100
connective tissue4.93e-11371
blood2.48e-0915
haemolymphatic fluid2.48e-0915
organism substance2.48e-0915
lateral plate mesoderm4.45e-09203
Disease
Ontology termp-valuen
hematologic cancer6.82e-1751
immune system cancer6.82e-1751
leukemia7.90e-1439
myeloid leukemia4.35e-1231


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.443649
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
MA0028.10.550763
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
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.12.31526
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.214613
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
MA0107.10.453492
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
MA0002.20.379056
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
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.11.37853
MA0164.10.90014
MA0080.21.32578
MA0018.20.870662
MA0099.20.7872
MA0079.20.476674
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
EBF1#187936.679850134926750.005184294118278910.0240363354975997
MAX#414934.839416631755340.01315737137836840.0466000647512688
SPI1#668848.204323508522730.000220661881527680.00249169707480478



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.