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Coexpression cluster:C3185

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Full id: C3185_chronic_acute_thymus_CD4_Hodgkin_CD8_NK



Phase1 CAGE Peaks

Hg19::chr11:6424016..6424033,-p7@APBB1
Hg19::chr4:108969174..108969197,-p@chr4:108969174..108969197
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Hg19::chr7:142498763..142498785,+p3@AJ568018


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

GO IDGO nameFDR corrected p-value
GO:0050760negative regulation of thymidylate synthase biosynthetic process0.00237450449389693
GO:0050758regulation of thymidylate synthase biosynthetic process0.00237450449389693
GO:0050757thymidylate synthase biosynthetic process0.00237450449389693
GO:0045749negative regulation of S phase of mitotic cell cycle0.0123009907713758
GO:0001540beta-amyloid binding0.0123009907713758
GO:0007090regulation of S phase of mitotic cell cycle0.0123009907713758
GO:0045930negative regulation of progression through mitotic cell cycle0.0123009907713758
GO:0033261regulation of progression through S phase0.0123009907713758
GO:0000084S phase of mitotic cell cycle0.0123009907713758
GO:0030426growth cone0.0123009907713758
GO:0030427site of polarized growth0.0123009907713758
GO:0051320S phase0.0124624789486762
GO:0007346regulation of progression through mitotic cell cycle0.0175268017854181
GO:0030027lamellipodium0.0194594735801954
GO:0017148negative regulation of translation0.0194594735801954
GO:0031327negative regulation of cellular biosynthetic process0.0200219068535414
GO:0009890negative regulation of biosynthetic process0.0202299818924186
GO:0030308negative regulation of cell growth0.0202299818924186
GO:0045792negative regulation of cell size0.0202299818924186
GO:0045926negative regulation of growth0.0217075291219072
GO:0031252leading edge0.0243979520439284
GO:0051329interphase of mitotic cell cycle0.0274886381140926
GO:0051325interphase0.0275265936430817
GO:0009615response to virus0.0275265936430817
GO:0007050cell cycle arrest0.0275265936430817
GO:0051248negative regulation of protein metabolic process0.0275265936430817
GO:0048771tissue remodeling0.0275265936430817
GO:0007409axonogenesis0.0275265936430817
GO:0045087innate immune response0.0275265936430817
GO:0048667neuron morphogenesis during differentiation0.0275265936430817
GO:0048812neurite morphogenesis0.0275265936430817
GO:0000904cellular morphogenesis during differentiation0.0279972299614313
GO:0031175neurite development0.0290841708536053
GO:0048666neuron development0.0321926668132127
GO:0001558regulation of cell growth0.0327848518702859
GO:0006417regulation of translation0.0327848518702859
GO:0031326regulation of cellular biosynthetic process0.0327848518702859
GO:0016049cell growth0.0327848518702859
GO:0040008regulation of growth0.0327848518702859
GO:0032990cell part morphogenesis0.0327848518702859
GO:0030030cell projection organization and biogenesis0.0327848518702859
GO:0048858cell projection morphogenesis0.0327848518702859
GO:0008361regulation of cell size0.0327848518702859
GO:0051707response to other organism0.0327848518702859
GO:0030182neuron differentiation0.0327848518702859
GO:0032501multicellular organismal process0.0327848518702859
GO:0009889regulation of biosynthetic process0.0327848518702859
GO:0045786negative regulation of progression through cell cycle0.0332813801169429
GO:0048699generation of neurons0.0350566403475582
GO:0022008neurogenesis0.0371838177210064
GO:0009607response to biotic stimulus0.0396941228186807
GO:0006954inflammatory response0.0396941228186807
GO:0005125cytokine activity0.0411003848729342
GO:0042995cell projection0.0411003848729342
GO:0000278mitotic cell cycle0.0420210337736801
GO:0051704multi-organism process0.0421524736917254
GO:0000074regulation of progression through cell cycle0.0438597620073579
GO:0051726regulation of cell cycle0.0438597620073579
GO:0022403cell cycle phase0.044310832096655
GO:0031324negative regulation of cellular metabolic process0.0449813148471854
GO:0051246regulation of protein metabolic process0.0482182281231848
GO:0009611response to wounding0.0482182281231848
GO:0008134transcription factor binding0.0482182281231848
GO:0009892negative regulation of metabolic process0.0482182281231848



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
T cell9.89e-4625
pro-T cell9.89e-4625
lymphocyte1.57e-4053
common lymphoid progenitor1.57e-4053
mature alpha-beta T cell7.67e-3918
alpha-beta T cell7.67e-3918
immature T cell7.67e-3918
mature T cell7.67e-3918
immature alpha-beta T cell7.67e-3918
lymphoid lineage restricted progenitor cell7.69e-3952
nucleate cell1.03e-3855
CD8-positive, alpha-beta T cell2.53e-2211
nongranular leukocyte9.18e-20115
leukocyte1.20e-18136
CD4-positive, alpha-beta T cell3.87e-166
hematopoietic stem cell6.27e-15168
angioblastic mesenchymal cell6.27e-15168
hematopoietic cell1.67e-14177
hematopoietic lineage restricted progenitor cell7.89e-14120
hematopoietic oligopotent progenitor cell4.77e-12161
hematopoietic multipotent progenitor cell4.77e-12161
naive T cell9.29e-093
single nucleate cell2.92e-083
mononuclear cell2.92e-083
natural killer cell9.23e-083
pro-NK cell9.23e-083
Uber Anatomy
Ontology termp-valuen
blood1.11e-1415
haemolymphatic fluid1.11e-1415
organism substance1.11e-1415
hemopoietic organ1.36e-127
immune organ1.36e-127
thymus4.18e-114
hemolymphoid system gland4.18e-114
thymic region4.18e-114
pharyngeal gland4.18e-114
thymus primordium4.18e-114
entire pharyngeal arch endoderm1.22e-0711
early pharyngeal endoderm1.22e-0711
pharyngeal epithelium2.26e-076


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.11.70014
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.11.55117
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0373086
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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

No analysis results for this cluster

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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