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Coexpression cluster:C270: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.160483,0.0154091,0.0561401,0.365837,0.106443,1.01127,0.234027,1.30097,0.128483,0.00961291,0.132352,0.282818,0.0305316,0.0616229,0.223288,0.129239,0.519219,0.259462,0.159054,0.11844,1.48483,0.00322747,0.629024,0.3842,0.210263,0.0929833,0.171168,0.037991,0.23127,0.0353963,0.276885,0.197381,0.189803,0.0722697,0.168105,0.0117293,0.072932,1.01562,0.24529,0.00436737,0.304392,0.251982,0.0501969,0.220604,0.0116534,0.371351,0.0662528,0.0300275,0.110285,0.231502,0.327266,0.248102,0.536441,0.247767,0.944688,0.0626855,0.651827,0.746518,0.073609,0.42365,0.223708,0.237772,0.368562,0.479385,0.93083,0.139488,0.429731,1.77697,0.190914,0.605197,0.0934092,0.581373,0.00455759,0.941267,0.0280311,0.0217876,0.0826908,0.455603,0.553282,0.0788978,0.169245,0.158049,1.39311,0.386221,0.318873,7.3646e-06,0.000528619,0.311681,0.360104,0.843833,1.26546,0.809396,0.599041,1.01605,0.0371708,0.121547,0.260328,0.235965,0.114082,0.0486817,0.865205,0.20442,1.223,0.524564,0.823969,0.304461,0.167668,0.47547,0.082662,0.0307933,0.0129891,0.230385,0.502787,0.594361,0.467098,0.98256,0.0136522,0.510941,0.428184,0.108465,0.927131,0.723102,0.155997,0.569873,0.561394,0.456665,0.227217,0.21123,1.00037,0.234154,0.299453,0.281363,0.396189,1.42561,0.518478,0.18393,0.267623,0.346797,1.21209,1.28061,0.893079,0.45145,0.852912,0.233601,0.134252,0.409931,0.125518,1.1257,0.100329,0.335138,0.32266,8.16553e-05,0.811167,0.704921,0.0669607,0.632367,0.33955,0.360544,0.405344,0.0653729,0.450446,0.286304,0.552112,0.176406,0.440079,0.545225,0.0100107,0.0653487,0.000297197
|tfbs_overrepresentation_for_novel_motifs=0.160483,0.0154091,0.0561401,0.365837,0.106443,1.01127,0.234027,1.30097,0.128483,0.00961291,0.132352,0.282818,0.0305316,0.0616229,0.223288,0.129239,0.519219,0.259462,0.159054,0.11844,1.48483,0.00322747,0.629024,0.3842,0.210263,0.0929833,0.171168,0.037991,0.23127,0.0353963,0.276885,0.197381,0.189803,0.0722697,0.168105,0.0117293,0.072932,1.01562,0.24529,0.00436737,0.304392,0.251982,0.0501969,0.220604,0.0116534,0.371351,0.0662528,0.0300275,0.110285,0.231502,0.327266,0.248102,0.536441,0.247767,0.944688,0.0626855,0.651827,0.746518,0.073609,0.42365,0.223708,0.237772,0.368562,0.479385,0.93083,0.139488,0.429731,1.77697,0.190914,0.605197,0.0934092,0.581373,0.00455759,0.941267,0.0280311,0.0217876,0.0826908,0.455603,0.553282,0.0788978,0.169245,0.158049,1.39311,0.386221,0.318873,7.3646e-06,0.000528619,0.311681,0.360104,0.843833,1.26546,0.809396,0.599041,1.01605,0.0371708,0.121547,0.260328,0.235965,0.114082,0.0486817,0.865205,0.20442,1.223,0.524564,0.823969,0.304461,0.167668,0.47547,0.082662,0.0307933,0.0129891,0.230385,0.502787,0.594361,0.467098,0.98256,0.0136522,0.510941,0.428184,0.108465,0.927131,0.723102,0.155997,0.569873,0.561394,0.456665,0.227217,0.21123,1.00037,0.234154,0.299453,0.281363,0.396189,1.42561,0.518478,0.18393,0.267623,0.346797,1.21209,1.28061,0.893079,0.45145,0.852912,0.233601,0.134252,0.409931,0.125518,1.1257,0.100329,0.335138,0.32266,8.16553e-05,0.811167,0.704921,0.0669607,0.632367,0.33955,0.360544,0.405344,0.0653729,0.450446,0.286304,0.552112,0.176406,0.440079,0.545225,0.0100107,0.0653487,0.000297197
|tfbs_overrepresentation_jaspar=MA0003.1;6.60954e-09,MA0004.1;0.136707,MA0006.1;0.00675862,MA0007.1;0.121286,MA0009.1;0.742767,MA0014.1;6.64228e-07,MA0017.1;0.297891,MA0019.1;2.06848,MA0024.1;0.577549,MA0025.1;0.369772,MA0027.1;1.75714,MA0028.1;0.252155,MA0029.1;1.14305,MA0030.1;0.204025,MA0031.1;0.164354,MA0038.1;0.066892,MA0040.1;0.215238,MA0041.1;0.633185,MA0042.1;0.869248,MA0043.1;0.269896,MA0046.1;0.261967,MA0048.1;0.0696187,MA0050.1;0.0308466,MA0051.1;0.0652924,MA0052.1;1.16764,MA0055.1;0.166259,MA0056.1;0,MA0057.1;0.0130668,MA0058.1;0.178154,MA0059.1;0.0142952,MA0060.1;0.0236409,MA0061.1;0.00353083,MA0063.1;0,MA0066.1;0.0670547,MA0067.1;0.521579,MA0068.1;0.0189264,MA0069.1;0.259258,MA0070.1;0.251448,MA0071.1;0.434692,MA0072.1;0.693601,MA0073.1;0.000283965,MA0074.1;0.500254,MA0076.1;0.199249,MA0077.1;1.26386,MA0078.1;0.71186,MA0081.1;0.348848,MA0083.1;0.275031,MA0084.1;0.687356,MA0087.1;0.689686,MA0088.1;0.0260706,MA0089.1;0,MA0090.1;0.219387,MA0091.1;0.32487,MA0092.1;0.108472,MA0093.1;0.0373762,MA0095.1;0,MA0098.1;0,MA0100.1;0.252489,MA0101.1;0.0387481,MA0103.1;0.367773,MA0105.1;0.0088191,MA0106.1;0.0835951,MA0107.1;0.0150387,MA0108.2;0.489019,MA0109.1;0,MA0111.1;1.07639,MA0113.1;0.303852,MA0114.1;0.360401,MA0115.1;0.456937,MA0116.1;0.00253981,MA0117.1;0.296853,MA0119.1;0.31413,MA0122.1;0.316066,MA0124.1;0.422741,MA0125.1;0.355789,MA0130.1;0,MA0131.1;0.374131,MA0132.1;0,MA0133.1;0,MA0135.1;0.792648,MA0136.1;0.0696103,MA0139.1;0.0727366,MA0140.1;0.0521172,MA0141.1;0.0662374,MA0142.1;0.878983,MA0143.1;0.304067,MA0144.1;0.00166309,MA0145.1;0.000878866,MA0146.1;0.00198936,MA0147.1;0.00269963,MA0148.1;0.158679,MA0149.1;0.0489541,MA0062.2;0.0364967,MA0035.2;0.192816,MA0039.2;3.55094e-07,MA0138.2;0.108774,MA0002.2;0.914249,MA0137.2;0.0459359,MA0104.2;0.0062078,MA0047.2;0.569671,MA0112.2;0.00224311,MA0065.2;0.120464,MA0150.1;0.0832005,MA0151.1;0,MA0152.1;0.0543283,MA0153.1;0.342762,MA0154.1;0.0026915,MA0155.1;0.00171258,MA0156.1;0.130599,MA0157.1;0.131206,MA0158.1;0,MA0159.1;0.0548544,MA0160.1;0.172887,MA0161.1;0,MA0162.1;3.71162e-05,MA0163.1;0.000184643,MA0164.1;0.319119,MA0080.2;0.0374118,MA0018.2;0.28579,MA0099.2;0.05445,MA0079.2;1.14755e-14,MA0102.2;0.721284,MA0258.1;0.0332469,MA0259.1;0.00311337,MA0442.1;0
}}
}}

Revision as of 18:55, 22 January 2013


Full id: C270_CD4_Fibroblast_acute_iPS_Aortic_CD34_Smooth



Phase1 CAGE Peaks

Hg19::chr10:70259244..70259249,+p1@ENST00000414397
Hg19::chr11:41559949..41559958,+p1@ENST00000489849
Hg19::chr11:8704298..8704345,+p1@RPL27A
Hg19::chr11:9780879..9780882,+p@chr11:9780879..9780882
+
Hg19::chr14:60630295..60630299,+p@chr14:60630295..60630299
+
Hg19::chr15:60696620..60696621,+p1@ENST00000477729
Hg19::chr16:3546164..3546173,+p1@ENST00000459875
Hg19::chr17:26794793..26794802,+p1@RPS7P1
Hg19::chr17:60474725..60474735,+p1@ENST00000466210
Hg19::chr19:20235787..20235812,+p1@ENST00000497576
Hg19::chr1:166716552..166716571,+p1@ENST00000447259
Hg19::chr1:77594751..77594764,+p1@ENST00000535687
Hg19::chr20:36073953..36073967,-p1@RPL7AP14
Hg19::chr20:42281142..42281149,+p1@RPL27AP
Hg19::chr20:45700487..45700491,+p1@ENST00000429337
Hg19::chr22:17673737..17673768,+p1@ENST00000428401
Hg19::chr22:32435449..32435460,+p1@ENST00000423610
Hg19::chr2:162944750..162944764,+p1@EIF3EP2
Hg19::chr2:44497668..44497671,+p1@ENST00000429825
Hg19::chr3:186617869..186617872,+p1@ENST00000412545
Hg19::chr3:39448201..39448222,+p1@RPSA
Hg19::chr3:54660217..54660228,+p1@RPS15P5
Hg19::chr4:152020789..152020800,+p3@RPS3A
Hg19::chr4:153356096..153356098,+p@chr4:153356096..153356098
+
Hg19::chr4:165864400..165864421,+p1@NACA3P
Hg19::chr4:25680438..25680449,+p1@ENST00000496507
Hg19::chr4:63376074..63376080,+p1@HMGN1P11
Hg19::chr5:10488861..10488883,+p1@ENST00000479312
Hg19::chr5:18049555..18049568,+p1@ENST00000490372
Hg19::chr5:31923400..31923411,+p1@ENST00000506046
Hg19::chr5:78825099..78825108,+p1@ENST00000486157
Hg19::chr6:121702579..121702585,+p1@ENST00000407291
Hg19::chr6:127756747..127756759,+p1@ENST00000404780
Hg19::chr6:151420592..151420605,+p1@ENST00000405720
Hg19::chr6:35436167..35436194,+p1@RPL10A
Hg19::chr7:102395576..102395578,+p1@ENST00000434317
Hg19::chr7:108150654..108150657,+p1@ENST00000457119
Hg19::chr7:135344733..135344758,+p1@ENST00000422772
p1@ENST00000431303
Hg19::chr7:138373682..138373693,+p1@ENST00000417063
Hg19::chr7:143493344..143493345,+p1@ENST00000421443
Hg19::chr8:102381085..102381119,+p1@NACAP1
Hg19::chr8:49297099..49297111,+p1@RPL29P19
Hg19::chr8:57500935..57500955,+p1@ENST00000464216
Hg19::chr9:129387943..129387948,+p@chr9:129387943..129387948
+
Hg19::chr9:135894802..135894817,+p1@EEF1A1P5
Hg19::chrX:114937108..114937121,+p1@ENST00000434365
Hg19::chrX:127913853..127913854,+p@chrX:127913853..127913854
+
Hg19::chrX:23855458..23855463,-p1@RPL9P7


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

p.valueFDRnGenesnPathwayName
4.90229198376432e-081.6209449566465e-05492Ribosome (KEGG):03010
5.12146905733492e-081.6209449566465e-05493Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
5.25198167428927e-060.0005540840666375184296Metabolism of proteins (Reactome):REACT_17015
1.16497041393593e-072.45808757340482e-054114Regulation of beta-cell development (Reactome):REACT_13698
2.10211562007729e-050.001663298984386164421Gene Expression (Reactome):REACT_71
6.46639354150921e-060.0005847467302536194312Diabetes pathways (Reactome):REACT_15380
2.89688180900988e-073.66745237020651e-054143Influenza Infection (Reactome):REACT_6167
2.51142294146909e-073.66745237020651e-054138{RPS27A,138} (Static Module):NA



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:0005830cytosolic ribosome (sensu Eukaryota)9.0654986515383e-06
GO:0003735structural constituent of ribosome4.17649681473539e-05
GO:0044445cytosolic part4.17649681473539e-05
GO:0005840ribosome4.17649681473539e-05
GO:0033279ribosomal subunit4.92998464617523e-05
GO:0030529ribonucleoprotein complex8.94157392872627e-05
GO:0006412translation9.6857364533907e-05
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)0.000106742572989642
GO:0009059macromolecule biosynthetic process0.000210778053192807
GO:0005829cytosol0.000399030908876565
GO:0044249cellular biosynthetic process0.000403158389548532
GO:0015935small ribosomal subunit0.000866415102296869
GO:0009058biosynthetic process0.000866415102296869
GO:0043232intracellular non-membrane-bound organelle0.00148830839864719
GO:0043228non-membrane-bound organelle0.00148830839864719
GO:0005055laminin receptor activity0.001618885021312
GO:0032991macromolecular complex0.00400855438096035
GO:0044444cytoplasmic part0.00727027070458189
GO:0010467gene expression0.0133971702269967
GO:0044267cellular protein metabolic process0.0139360835017471
GO:0044260cellular macromolecule metabolic process0.0139432706096868
GO:0019538protein metabolic process0.015231654652785
GO:0005842cytosolic large ribosomal subunit (sensu Eukaryota)0.0219127406722634
GO:0003723RNA binding0.0284036073634093
GO:0008305integrin complex0.0284036073634093
GO:0005737cytoplasm0.0327837559577845
GO:0006413translational initiation0.0450399050801686
GO:0044446intracellular organelle part0.0450399050801686
GO:0044422organelle part0.0450399050801686
GO:0015934large ribosomal subunit0.0450547311984884
GO:0043235receptor complex0.0456641632581076



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 lineage restricted progenitor cell1.45e-22120
classical monocyte6.99e-2142
CD14-positive, CD16-negative classical monocyte6.99e-2142
hematopoietic stem cell3.43e-20168
angioblastic mesenchymal cell3.43e-20168
nongranular leukocyte1.47e-19115
leukocyte1.84e-19136
hematopoietic oligopotent progenitor cell1.91e-19161
hematopoietic multipotent progenitor cell1.91e-19161
hematopoietic cell2.28e-19177
defensive cell3.36e-1848
phagocyte3.36e-1848
native cell1.18e-17722
myeloid lineage restricted progenitor cell6.69e-1366
animal cell7.74e-13679
eukaryotic cell7.74e-13679
granulocyte monocyte progenitor cell3.38e-1267
macrophage dendritic cell progenitor3.99e-1261
stuff accumulating cell1.18e-1187
monopoietic cell3.82e-1159
monocyte3.82e-1159
monoblast3.82e-1159
promonocyte3.82e-1159
myeloid cell1.11e-10108
common myeloid progenitor1.11e-10108
stem cell1.28e-10441
somatic cell2.24e-10588
multi fate stem cell4.38e-10427
nucleate cell4.91e-1055
somatic stem cell1.10e-09433
lymphocyte3.53e-0953
common lymphoid progenitor3.53e-0953
lymphoid lineage restricted progenitor cell4.80e-0952
myeloid leukocyte1.33e-0872
connective tissue cell1.84e-08361
mesenchymal cell2.67e-08354
motile cell1.15e-07386
Uber Anatomy
Ontology termp-valuen
skeletal element2.96e-1190
bone marrow3.29e-1176
bone element1.31e-1082
skeletal system3.33e-09100
immune system3.95e-0893
hematopoietic system4.67e-0898
blood island4.67e-0898
musculoskeletal system1.68e-07167
connective tissue1.81e-07371
hemolymphoid system4.18e-07108


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)
MA0003.16.60954e-09
MA0004.10.136707
MA0006.10.00675862
MA0007.10.121286
MA0009.10.742767
MA0014.16.64228e-07
MA0017.10.297891
MA0019.12.06848
MA0024.10.577549
MA0025.10.369772
MA0027.11.75714
MA0028.10.252155
MA0029.11.14305
MA0030.10.204025
MA0031.10.164354
MA0038.10.066892
MA0040.10.215238
MA0041.10.633185
MA0042.10.869248
MA0043.10.269896
MA0046.10.261967
MA0048.10.0696187
MA0050.10.0308466
MA0051.10.0652924
MA0052.11.16764
MA0055.10.166259
MA0056.10
MA0057.10.0130668
MA0058.10.178154
MA0059.10.0142952
MA0060.10.0236409
MA0061.10.00353083
MA0063.10
MA0066.10.0670547
MA0067.10.521579
MA0068.10.0189264
MA0069.10.259258
MA0070.10.251448
MA0071.10.434692
MA0072.10.693601
MA0073.10.000283965
MA0074.10.500254
MA0076.10.199249
MA0077.11.26386
MA0078.10.71186
MA0081.10.348848
MA0083.10.275031
MA0084.10.687356
MA0087.10.689686
MA0088.10.0260706
MA0089.10
MA0090.10.219387
MA0091.10.32487
MA0092.10.108472
MA0093.10.0373762
MA0095.10
MA0098.10
MA0100.10.252489
MA0101.10.0387481
MA0103.10.367773
MA0105.10.0088191
MA0106.10.0835951
MA0107.10.0150387
MA0108.20.489019
MA0109.10
MA0111.11.07639
MA0113.10.303852
MA0114.10.360401
MA0115.10.456937
MA0116.10.00253981
MA0117.10.296853
MA0119.10.31413
MA0122.10.316066
MA0124.10.422741
MA0125.10.355789
MA0130.10
MA0131.10.374131
MA0132.10
MA0133.10
MA0135.10.792648
MA0136.10.0696103
MA0139.10.0727366
MA0140.10.0521172
MA0141.10.0662374
MA0142.10.878983
MA0143.10.304067
MA0144.10.00166309
MA0145.10.000878866
MA0146.10.00198936
MA0147.10.00269963
MA0148.10.158679
MA0149.10.0489541
MA0062.20.0364967
MA0035.20.192816
MA0039.23.55094e-07
MA0138.20.108774
MA0002.20.914249
MA0137.20.0459359
MA0104.20.0062078
MA0047.20.569671
MA0112.20.00224311
MA0065.20.120464
MA0150.10.0832005
MA0151.10
MA0152.10.0543283
MA0153.10.342762
MA0154.10.0026915
MA0155.10.00171258
MA0156.10.130599
MA0157.10.131206
MA0158.10
MA0159.10.0548544
MA0160.10.172887
MA0161.10
MA0162.13.71162e-05
MA0163.10.000184643
MA0164.10.319119
MA0080.20.0374118
MA0018.20.28579
MA0099.20.05445
MA0079.21.14755e-14
MA0102.20.721284
MA0258.10.0332469
MA0259.10.00311337
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
RDBP#793639.602400249376560.003825246528919180.018876626452173



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

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