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{{Coexpression_clusters
{
|full_id=C1185_splenic_myeloma_lymphoma_immature_acute_CD19_Burkitt
|

Latest revision as of 11:39, 17 September 2013


Full id: C1185_splenic_myeloma_lymphoma_immature_acute_CD19_Burkitt



Phase1 CAGE Peaks

Hg19::chr12:9885606..9885619,-p4@CLECL1
Hg19::chr12:9885630..9885668,-p2@CLECL1
Hg19::chr12:9885678..9885698,-p3@CLECL1
Hg19::chr12:9885702..9885717,-p5@CLECL1
Hg19::chr12:9885767..9885808,-p1@CLECL1
Hg19::chr3:121796686..121796695,+p6@CD86
Hg19::chr3:121796697..121796747,+p2@CD86


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:0043016regulation of lymphotoxin A biosynthetic process0.00239759062769123
GO:0043017positive regulation of lymphotoxin A biosynthetic process0.00239759062769123
GO:0045630positive regulation of T-helper 2 cell differentiation0.00239759062769123
GO:0032641lymphotoxin A production0.00239759062769123
GO:0042109lymphotoxin A biosynthetic process0.00239759062769123
GO:0045404positive regulation of interleukin-4 biosynthetic process0.00239759062769123
GO:0042097interleukin-4 biosynthetic process0.00239759062769123
GO:0045402regulation of interleukin-4 biosynthetic process0.00239759062769123
GO:0045624positive regulation of T-helper cell differentiation0.00239759062769123
GO:0045628regulation of T-helper 2 cell differentiation0.00239759062769123
GO:0032633interleukin-4 production0.00239759062769123
GO:0045064T-helper 2 cell differentiation0.00274719882404461
GO:0045622regulation of T-helper cell differentiation0.00299672360703993
GO:0002285lymphocyte activation during immune response0.00299672360703993
GO:0002293alpha-beta T cell differentiation during immune response0.00299672360703993
GO:0002294CD4-positive, alpha-beta T cell differentiation during immune response0.00299672360703993
GO:0002292T cell differentiation during immune response0.00299672360703993
GO:0042093T-helper cell differentiation0.00299672360703993
GO:0002366leukocyte activation during immune response0.00299672360703993
GO:0042092T-helper 2 type immune response0.00299672360703993
GO:0002286T cell activation during immune response0.00299672360703993
GO:0002263cell activation during immune response0.00299672360703993
GO:0043367CD4-positive, alpha beta T cell differentiation0.0030216518232285
GO:0045086positive regulation of interleukin-2 biosynthetic process0.0030216518232285
GO:0045076regulation of interleukin-2 biosynthetic process0.00376697693989987
GO:0046632alpha-beta T cell differentiation0.00376697693989987
GO:0015026coreceptor activity0.00376697693989987
GO:0042094interleukin-2 biosynthetic process0.00376697693989987
GO:0046631alpha-beta T cell activation0.00431884315484041
GO:0032623interleukin-2 production0.00461420708182391
GO:0042108positive regulation of cytokine biosynthetic process0.00844316002446495
GO:0030217T cell differentiation0.00844316002446495
GO:0045727positive regulation of translation0.0105817211871921
GO:0042035regulation of cytokine biosynthetic process0.0112936105942213
GO:0031328positive regulation of cellular biosynthetic process0.0112936105942213
GO:0030098lymphocyte differentiation0.011711202345814
GO:0042089cytokine biosynthetic process0.0117875550671227
GO:0042107cytokine metabolic process0.0117875550671227
GO:0009891positive regulation of biosynthetic process0.0118227649235901
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0122089120025065
GO:0002250adaptive immune response0.0122089120025065
GO:0051247positive regulation of protein metabolic process0.0133278245401661
GO:0002521leukocyte differentiation0.0137826168697267
GO:0042110T cell activation0.0146649241795027
GO:0001816cytokine production0.0165301320416057
GO:0045595regulation of cell differentiation0.0205975954769105
GO:0046649lymphocyte activation0.021695778430325
GO:0030097hemopoiesis0.022064169935319
GO:0048534hemopoietic or lymphoid organ development0.0232207415463573
GO:0045321leukocyte activation0.0232685887144564
GO:0002520immune system development0.0232685887144564
GO:0006417regulation of translation0.0232685887144564
GO:0031326regulation of cellular biosynthetic process0.0246851982290708
GO:0001775cell activation0.0254417994942434
GO:0009889regulation of biosynthetic process0.0259323005627626
GO:0008284positive regulation of cell proliferation0.0272056617714807
GO:0050793regulation of developmental process0.0272056617714807
GO:0045941positive regulation of transcription0.031588023573144
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0321608772250949
GO:0016563transcription activator activity0.0338034384215129
GO:0005529sugar binding0.0373172139940967
GO:0031325positive regulation of cellular metabolic process0.0386095807151983
GO:0009893positive regulation of metabolic process0.0406876863975909
GO:0051246regulation of protein metabolic process0.0432075775958719
GO:0042127regulation of cell proliferation0.0472481184952243
GO:0030246carbohydrate binding0.0474188548497282



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 stem cell2.02e-82168
angioblastic mesenchymal cell2.02e-82168
hematopoietic cell5.61e-81177
hematopoietic oligopotent progenitor cell1.29e-78161
hematopoietic multipotent progenitor cell1.29e-78161
leukocyte1.80e-66136
hematopoietic lineage restricted progenitor cell2.12e-58120
nongranular leukocyte4.05e-58115
myeloid cell8.37e-46108
common myeloid progenitor8.37e-46108
granulocyte monocyte progenitor cell2.86e-3067
lymphocyte of B lineage5.94e-3024
pro-B cell5.94e-3024
macrophage dendritic cell progenitor3.34e-2861
lymphocyte4.03e-2853
common lymphoid progenitor4.03e-2853
myeloid lineage restricted progenitor cell2.41e-2766
lymphoid lineage restricted progenitor cell7.34e-2752
myeloid leukocyte1.21e-2672
nucleate cell1.29e-2655
monopoietic cell6.34e-2659
monocyte6.34e-2659
monoblast6.34e-2659
promonocyte6.34e-2659
defensive cell2.12e-2448
phagocyte2.12e-2448
classical monocyte3.21e-2242
CD14-positive, CD16-negative classical monocyte3.21e-2242
mesenchymal cell3.77e-21354
connective tissue cell4.10e-20361
B cell1.09e-1714
motile cell1.66e-16386
dendritic cell4.48e-1410
multi fate stem cell3.28e-12427
conventional dendritic cell6.31e-128
somatic stem cell1.24e-11433
stem cell6.85e-11441
stuff accumulating cell9.33e-0987
immature conventional dendritic cell1.12e-085
common dendritic progenitor1.12e-085
CD8-positive, alpha-beta T cell4.77e-0811
Langerhans cell1.42e-075
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.52e-3898
blood island4.52e-3898
hemolymphoid system1.18e-35108
immune system1.02e-2793
bone marrow1.50e-2676
bone element1.69e-2382
skeletal element4.35e-2090
connective tissue2.59e-19371
skeletal system1.23e-16100
lateral plate mesoderm2.06e-09203
blood6.08e-0915
haemolymphatic fluid6.08e-0915
organism substance6.08e-0915
Disease
Ontology termp-valuen
hematologic cancer1.96e-1851
immune system cancer1.96e-1851
leukemia6.99e-1439
myeloid leukemia1.19e-1331
lymphoma2.10e-0710


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)
MA0003.10.00215847
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0723474
MA0017.10.380797
MA0019.11.57204
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.13.62793
MA0048.10.120314
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.12.43031
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.000265001
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.11.64331
MA0103.10.332048
MA0105.11.14871
MA0106.10.648997
MA0107.13.85586
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.11.491
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.0807715
MA0146.10.0127148
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.00276064
MA0138.20.704862
MA0002.22.53691
MA0137.20.36398
MA0104.20.223944
MA0047.21.53797
MA0112.20.0758925
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.10.071478
MA0156.10.959643
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.0167306
MA0164.10.678332
MA0080.23.39674
MA0018.20.650405
MA0099.20.572
MA0079.29.15802e-07
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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
BATF#10538517.39842985164552.2818035468994e-068.13897816375092e-05
NFKB1#479075.488063424193846.66568321176054e-060.000194783796573324
POLR2A#543072.147453176558070.004747636447610280.0223350631960347
SPI1#668878.204323508522733.99342038048841e-071.93266372158401e-05



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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