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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:26, 17 September 2013


Full id: C600_Reticulocytes_CD34_HES3GFP_Hep2_Mesenchymal_iPS_CD4



Phase1 CAGE Peaks

Hg19::chr17:77429187..77429190,+p@chr17:77429187..77429190
+
Hg19::chr18:23751305..23751327,-p1@ENST00000307796
Hg19::chr1:120904659..120904667,+p1@ENST00000401004
Hg19::chr1:120905986..120906002,+p1@HIST2H2BA
Hg19::chr1:149804218..149804222,+p11@HIST2H4A
p11@HIST2H4B
Hg19::chr1:149812975..149812992,+p@chr1:149812975..149812992
+
Hg19::chr1:149822620..149822635,+p1@HIST2H2AA3
p1@HIST2H2AA4
Hg19::chr1:149824160..149824183,+p1@HIST2H3A
p1@HIST2H3C
p1@HIST2H3D
Hg19::chr21:44985053..44985072,+p1@uc002zdj.1
Hg19::chr22:51142547..51142550,-p@chr22:51142547..51142550
-
Hg19::chr2:175366659..175366666,+p1@ENST00000313760
p1@ENST00000545980
Hg19::chr6:27776055..27776066,+p19@HIST1H3H
Hg19::chr6:27791862..27791877,+p10@HIST1H4C
p10@HIST1H4F
p9@HIST1H4A
p9@HIST1H4B
p9@HIST1H4D
p9@HIST1H4E
p9@HIST1H4H
p9@HIST1H4I
p9@HIST1H4J
p9@HIST1H4K
p9@HIST1H4L
p9@HIST2H4A
p9@HIST2H4B
p9@HIST4H4
Hg19::chr6:32146268..32146280,+p2@RNF5
Hg19::chrX:57301700..57301701,+p@chrX:57301700..57301701
+


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:0000786nucleosome1.02889990100262e-05
GO:0006334nucleosome assembly1.82795360157763e-05
GO:0031497chromatin assembly1.82795360157763e-05
GO:0006333chromatin assembly or disassembly2.69989057737589e-05
GO:0065004protein-DNA complex assembly2.69989057737589e-05
GO:0000785chromatin3.35101398552361e-05
GO:0006325establishment and/or maintenance of chromatin architecture6.68254071514103e-05
GO:0006323DNA packaging6.68254071514103e-05
GO:0044427chromosomal part6.68254071514103e-05
GO:0005694chromosome8.42194242363336e-05
GO:0051276chromosome organization and biogenesis8.42194242363336e-05
GO:0065003macromolecular complex assembly0.000215905675290121
GO:0022607cellular component assembly0.000247612823251949
GO:0006259DNA metabolic process0.000826583373718418
GO:0006996organelle organization and biogenesis0.00139878014476753
GO:0043234protein complex0.00791414839995249
GO:0043232intracellular non-membrane-bound organelle0.00791414839995249
GO:0043228non-membrane-bound organelle0.00791414839995249
GO:0043283biopolymer metabolic process0.00941767443590979
GO:0016043cellular component organization and biogenesis0.00998393556166264
GO:0003677DNA binding0.0115816774323599
GO:0032991macromolecular complex0.0148845201490435
GO:0044446intracellular organelle part0.0163198533038729
GO:0044422organelle part0.0163198533038729
GO:0043170macromolecule metabolic process0.0277801155833588
GO:0048015phosphoinositide-mediated signaling0.0348538768688054
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0394742815323511
GO:0044237cellular metabolic process0.0398442130585918
GO:0005634nucleus0.0398442130585918
GO:0044238primary metabolic process0.0398442130585918
GO:0003676nucleic acid binding0.0439843809381516



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
hematopoietic oligopotent progenitor cell2.61e-14161
hematopoietic multipotent progenitor cell2.61e-14161
hematopoietic stem cell1.36e-13168
angioblastic mesenchymal cell1.36e-13168
hematopoietic lineage restricted progenitor cell2.16e-13120
classical monocyte1.16e-1242
CD14-positive, CD16-negative classical monocyte1.16e-1242
myeloid cell1.21e-12108
common myeloid progenitor1.21e-12108
defensive cell4.03e-1248
phagocyte4.03e-1248
leukocyte5.29e-12136
hematopoietic cell7.47e-12177
myeloid lineage restricted progenitor cell4.07e-1166
granulocyte monocyte progenitor cell1.13e-1067
myeloid leukocyte1.17e-0972
macrophage dendritic cell progenitor4.24e-0961
nongranular leukocyte1.32e-08115
stuff accumulating cell2.83e-0887
monopoietic cell6.70e-0859
monocyte6.70e-0859
monoblast6.70e-0859
promonocyte6.70e-0859
Uber Anatomy
Ontology termp-valuen
larynx5.10e-129
bone marrow2.00e-1076
skeletal element8.98e-1090
immune system1.87e-0993
bone element1.95e-0982
skeletal system3.91e-08100
upper respiratory tract9.09e-0819
hematopoietic system4.35e-0798
blood island4.35e-0798


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)
MA0003.10.0132214
MA0004.10.256222
MA0006.10.137644
MA0007.10.241375
MA0009.10.669377
MA0014.10.0332175
MA0017.10.16476
MA0019.10.990457
MA0024.14.71606
MA0025.10.796882
MA0027.12.25966
MA0028.10.454219
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.27117
MA0042.10.245557
MA0043.11.60692
MA0046.10.659066
MA0048.10.23222
MA0050.11.27601
MA0051.10.896276
MA0052.11.45703
MA0055.10.120131
MA0056.10
MA0057.10.0873069
MA0058.10.182945
MA0059.10.182001
MA0060.13.03943
MA0061.10.198509
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.10.0373092
MA0069.10.655419
MA0070.10.644843
MA0071.10.308534
MA0072.10.640598
MA0073.10.00474347
MA0074.10.337035
MA0076.10.567195
MA0077.10.633326
MA0078.10.424186
MA0081.10.18212
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.11669
MA0089.10
MA0090.10.593146
MA0091.10.258318
MA0092.10.228476
MA0093.10.139688
MA0095.10
MA0098.10
MA0100.10.353174
MA0101.10.861002
MA0103.10.131472
MA0105.10.0162551
MA0106.10.37688
MA0107.10.315431
MA0108.22.21312
MA0109.10
MA0111.10.215855
MA0113.10.39123
MA0114.10.636237
MA0115.10.900969
MA0116.10.0971018
MA0117.10.705104
MA0119.10.170362
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.11.66629
MA0136.10.347318
MA0139.10.0481205
MA0140.10.30631
MA0141.10.180729
MA0142.10.489543
MA0143.10.391385
MA0144.10.0838502
MA0145.10.00981909
MA0146.10.114035
MA0147.10.0991954
MA0148.10.276339
MA0149.10.298252
MA0062.20.191053
MA0035.20.305721
MA0039.20.0182366
MA0138.20.425279
MA0002.20.0612545
MA0137.20.153033
MA0104.20.0667907
MA0047.20.366327
MA0112.20.124752
MA0065.20.287056
MA0150.10.201098
MA0151.10
MA0152.10.838393
MA0153.10.763487
MA0154.10.0723831
MA0155.10.0077078
MA0156.10.154615
MA0157.10.46471
MA0158.10
MA0159.10.0995776
MA0160.10.288813
MA0161.10
MA0162.10.0243066
MA0163.10.0128736
MA0164.12.74285
MA0080.20.139746
MA0018.20.98566
MA0099.20.312108
MA0079.20.000244312
MA0102.21.1957
MA0258.10.0785319
MA0259.10.104286
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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