Personal tools

Coexpression cluster:C1677

From FANTOM5_SSTAR

Jump to: navigation, search


Full id: C1677_acute_CD34_CD133_chronic_Whole_leukemia_myelodysplastic



Phase1 CAGE Peaks

  Short description
Hg19::chr12:54694979..54694993,+ p2@COPZ1
Hg19::chr21:21630930..21630941,- p3@ENST00000436373
Hg19::chr21:21630952..21630969,- p2@ENST00000436373
Hg19::chr21:21630981..21630991,- p4@ENST00000436373
Hg19::chr21:21630994..21631007,- p1@ENST00000436373


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:0006890retrograde vesicle-mediated transport, Golgi to ER0.00610502766984575
GO:0030126COPI vesicle coat0.00610502766984575
GO:0030663COPI coated vesicle membrane0.00610502766984575
GO:0006891intra-Golgi vesicle-mediated transport0.00610502766984575
GO:0030137COPI-coated vesicle0.00610502766984575
GO:0030120vesicle coat0.0130822021496695
GO:0030662coated vesicle membrane0.0130822021496695
GO:0005798Golgi-associated vesicle0.0148777985231535
GO:0048193Golgi vesicle transport0.0148777985231535
GO:0030659cytoplasmic vesicle membrane0.0148777985231535
GO:0044433cytoplasmic vesicle part0.0148777985231535
GO:0012506vesicle membrane0.0148777985231535
GO:0030117membrane coat0.0148777985231535
GO:0048475coated membrane0.0148777985231535
GO:0030135coated vesicle0.0175968444601436
GO:0045045secretory pathway0.0269339456022607
GO:0032940secretion by cell0.0310279053338043
GO:0006461protein complex assembly0.0310279053338043
GO:0016023cytoplasmic membrane-bound vesicle0.0310279053338043
GO:0031988membrane-bound vesicle0.0310279053338043
GO:0000139Golgi membrane0.0310279053338043
GO:0046903secretion0.0310279053338043
GO:0044431Golgi apparatus part0.0310279053338043
GO:0031410cytoplasmic vesicle0.0310279053338043
GO:0031982vesicle0.0310279053338043
GO:0006886intracellular protein transport0.0365334800605023
GO:0016192vesicle-mediated transport0.0403011630493086
GO:0005794Golgi apparatus0.0445692671275504
GO:0065003macromolecular complex assembly0.0468093399432393
GO:0022607cellular component assembly0.0486606617214176
GO:0015031protein transport0.0486923487162438
GO:0005783endoplasmic reticulum0.0486923487162438
GO:0046907intracellular transport0.0486923487162438
GO:0045184establishment of protein localization0.0486923487162438
GO:0008104protein localization0.0493019461405191
GO:0033036macromolecule localization0.049888461403827
GO:0012505endomembrane system0.049888461403827



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


Uber Anatomy
Ontology termp-valuen
blood1.52e-1415
haemolymphatic fluid1.52e-1415
organism substance1.52e-1415
Disease
Ontology termp-valuen
myeloid leukemia4.45e-6231
leukemia1.34e-4839
hematologic cancer2.66e-3651
immune system cancer2.66e-3651
chronic leukemia2.67e-278
organ system cancer4.33e-11137
chronic myeloid leukemia5.58e-081
acute myeloid leukemia1.07e-071
syndrome1.15e-071


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)
MA0003.10.481059
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.15.789
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
MA0041.11.55893
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.12.53085
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.11.98392
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.12.45107
MA0073.10.111822
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.11.36977
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
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
MA0136.11.76068
MA0139.10.277033
MA0140.14.03435
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.22.78095
MA0039.20.15493
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.425004
MA0065.20.146576
MA0150.12.32613
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.00463
MA0160.11.60707
MA0161.10
MA0162.10.21472
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.00732454
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
CCNT2#90556.336201576962639.78880505817628e-050.001389228171587
ELF1#199743.406478367046030.01235066105299550.0447288539327899
EP300#203345.419153380978560.00209386927943890.0121133115645776
FOSL1#8061431.77086377309841.96715033715934e-067.22388235100509e-05
GATA1#2623410.84824651504040.0001390956917094380.00181542301255211
GATA2#2624410.19594538684320.0001775447777609820.00215661770697595
REST#597859.650028716128021.19441074361324e-050.000301311747952229
TAL1#6886423.89489334195226.10828383356726e-060.000181491623127719
USF1#739145.089199421766370.00266867775360040.0147148532763989



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.