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Coexpression cluster:C1704: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.787587,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,0.345702,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.969147,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.94379,0.27659,0.417272,0.432883,1.06371,0.654459,0.388123,0.301779,0.415749,0.580638,0.414516,0.451846,0.476793,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.659455,0.688844,1.04369,0.736968,0.86107,0.935408,1.78554,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.554326,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.796279,0.934302,0.755403,0.327263,1.18161,0.914416,0.49825,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,1.15465,0.381528,0.28626,1.06255,0.849074,0.606298,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,2.18702,0.717647,0.549347,1.11542,1.27602,1.05402,0.494368,0.631235,1.37132,0.412056,0.597842,1.45429,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,2.85991,0.763715,1.43285,0.629991,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,1.63047,0.87256,2.09294,0.577088,0.953361,1.00998,1.29319,1.15522,0.840171,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,1.65153,0.731946,0.443702
|tfbs_overrepresentation_jaspar=MA0003.1;0.0497246,MA0004.1;0.626788,MA0006.1;1.14863,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.161847,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;0.470679,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.569896,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;2.69304,MA0056.1;0,MA0057.1;0.189508,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.860776,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;2.7757,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.215829,MA0074.1;0.730989,MA0076.1;2.29573,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;1.2972,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.412364,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;0.175503,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;1.1512,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;0.759606,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.868598,MA0146.1;0.333008,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.777733,MA0035.2;0.691506,MA0039.2;0.527987,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.425004,MA0065.2;0.146576,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;0.130813,MA0156.1;1.20729,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.469165,MA0163.1;0.168633,MA0164.1;0.810347,MA0080.2;1.15604,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;0.475695,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;1.80881,MA0442.1;0
}}
}}

Revision as of 20:07, 22 January 2013


Full id: C1704_CD4_Dendritic_CD8_CD19_Natural_Basophils_Eosinophils



Phase1 CAGE Peaks

Hg19::chr13:28024374..28024401,+p@chr13:28024374..28024401
+
Hg19::chr15:50647015..50647042,-p2@FLJ10038
Hg19::chr2:55845029..55845079,+p@chr2:55845029..55845079
+
Hg19::chr6:42713792..42713847,-p1@TBCC
Hg19::chrX:106960429..106960457,+p@chrX:106960429..106960457
+


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:0007023post-chaperonin tubulin folding pathway0.00147180030613446
GO:0007025beta-tubulin folding0.00183975038266808
GO:0007021tubulin folding0.0022077004592017
GO:0051087chaperone binding0.00294360061226893
GO:0005874microtubule0.0423142588013658
GO:0006457protein folding0.0423142588013658



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 cell6.75e-40177
hematopoietic stem cell2.65e-39168
angioblastic mesenchymal cell2.65e-39168
leukocyte8.39e-37136
hematopoietic oligopotent progenitor cell2.41e-35161
hematopoietic multipotent progenitor cell2.41e-35161
hematopoietic lineage restricted progenitor cell1.75e-28120
nongranular leukocyte3.78e-27115
nucleate cell3.61e-1955
lymphocyte1.41e-1853
common lymphoid progenitor1.41e-1853
lymphoid lineage restricted progenitor cell3.12e-1852
myeloid cell8.44e-17108
common myeloid progenitor8.44e-17108
myeloid leukocyte1.56e-1372
mature alpha-beta T cell7.50e-1218
alpha-beta T cell7.50e-1218
immature T cell7.50e-1218
mature T cell7.50e-1218
immature alpha-beta T cell7.50e-1218
granulocyte monocyte progenitor cell4.48e-1167
T cell8.32e-1125
pro-T cell8.32e-1125
myeloid lineage restricted progenitor cell1.60e-1066
macrophage dendritic cell progenitor2.52e-0961
classical monocyte5.64e-0942
CD14-positive, CD16-negative classical monocyte5.64e-0942
monopoietic cell1.22e-0859
monocyte1.22e-0859
monoblast1.22e-0859
promonocyte1.22e-0859
B cell2.39e-0814
CD8-positive, alpha-beta T cell3.67e-0811
connective tissue cell8.91e-08361
mesenchymal cell1.51e-07354
lymphocyte of B lineage3.83e-0724
pro-B cell3.83e-0724
defensive cell4.43e-0748
phagocyte4.43e-0748
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.23e-1698
blood island2.23e-1698
hemolymphoid system2.73e-16108
immune system3.45e-1193
bone marrow8.20e-1076
bone element3.62e-0982
skeletal element8.91e-0890
blood2.16e-0715
haemolymphatic fluid2.16e-0715
organism substance2.16e-0715


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)
MA0003.10.0497246
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.10.161847
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
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.12.69304
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.860776
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.12.7757
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.215829
MA0074.10.730989
MA0076.12.29573
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
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
MA0136.10.743749
MA0139.10.759606
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.868598
MA0146.10.333008
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.777733
MA0035.20.691506
MA0039.20.527987
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.425004
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.11.20729
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.10.168633
MA0164.10.810347
MA0080.21.15604
MA0018.20.781393
MA0099.20.699641
MA0079.20.475695
MA0102.21.66336
MA0258.10.345771
MA0259.11.80881
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
CCNT2#90545.068961261570110.002709998091280770.0148931535811025
CHD2#110636.206413700470110.007774550126275590.0319483077174148
E2F1#186943.925911371903460.007214984547106360.0298721812136865
EGR1#195843.990543275848110.0067800983001440.0287614413634744
ELF1#199743.406478367046030.01235066105299550.0447304050252729
GABPB1#255345.654147068945740.001776696502096670.0109061012097375
GTF2B#2959212.77753197372970.00919936089559720.0347866342943363
GTF2F1#2962410.19172870140610.000177833889427640.00215837229261282
MAX#414945.16204440720570.002526309009485180.013996349617613
MEF2C#4208216.52454179704960.005579850077982050.0252416495124688
MYC#460944.177825497287520.005691969036823440.0256743350711239
NFKB1#479055.488063424193840.0002008162847462320.00238900238781315
POU2F2#545247.284899246194020.0006631223288743860.00542332285867752
REST#597835.790017229676810.009468788694433940.0356930203731317
SP1#666744.558705102512720.00407573565781680.019478595907506
SPI1#668846.563458806818180.0009957429636454020.00714100112477938
TAF1#687253.343046285745290.002394600090870310.0135242071647417
TAF7#687936.859841642954350.005843286407019040.0262423990136599
TAL1#6886211.94744667097610.0104757781809920.0388040360859948
TBP#690853.706770687096390.001428755106721120.00918093610969343
YY1#752843.928936599883080.007193866269917620.0298367896177247



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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