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Coexpression cluster:C419: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.0799767,0.0118854,0.0765276,0.471537,0.46447,0.154482,0.589869,0.225126,0.220756,0.0680542,0.136211,0.23459,0.519856,0.571162,0.801267,0.880879,0.372343,0.34735,0.170793,0.196115,0.949389,0.286209,0.149707,0.2061,0.098963,0.251049,0.44201,0.453775,0.215908,0.875098,0.123558,1.03951,0.523701,0.528541,0.0451802,0.776007,0.04405,0.155199,0.0362139,0.0160107,0.170767,0.114449,0.339281,1.21211,0.554832,0.0913173,0.204918,0.129869,0.641077,0.816752,0.261519,0.610973,0.259797,0.467708,0.602614,0.198331,0.481143,0.176558,0.605037,0.175903,1.11427,0.206544,1.40684,0.349892,0.21901,0.32251,0.683218,1.032,0.394058,0.876356,0.107303,0.0946548,0.00295624,0.600809,0.0107858,0.263319,0.407884,0.336375,0.39137,0.65413,0.351556,0.92151,0.218762,0.0921969,0.554704,0.000526382,0.00178341,0.36892,0.281033,1.1284,0.769994,0.530777,0.416714,0.296803,0.0586689,0.0343354,0.848106,0.452776,0.284531,0.745565,0.609943,0.41198,0.448017,0.375338,0.842156,0.133549,0.36244,0.56558,0.325637,0.0520752,0.279145,0.445659,0.257318,0.141815,0.725188,0.675638,0.0149019,0.122878,0.32067,0.554632,0.593343,0.279196,0.152778,0.226712,0.828974,0.33698,0.199838,0.420907,0.631927,0.58976,1.31627,0.788377,0.645033,0.637637,0.782074,0.345978,0.381933,0.148728,0.742365,1.57584,1.1795,0.707679,0.201014,0.449766,0.314855,0.171082,0.301898,1.41836,1.20253,0.290478,0.371294,0.00451953,0.531723,0.207168,0.20621,0.90553,0.268853,0.43378,0.326069,0.0845645,0.706553,0.515425,0.390719,0.291122,0.873572,0.218208,0.110299,0.587697,0.0101973
|tfbs_overrepresentation_jaspar=MA0003.1;0.000121805,MA0004.1;0.430931,MA0006.1;0.0576274,MA0007.1;0.128232,MA0009.1;0.495012,MA0014.1;0.00150727,MA0017.1;0.0747264,MA0019.1;0.238234,MA0024.1;0.404839,MA0025.1;0.614568,MA0027.1;2.05626,MA0028.1;0.0643724,MA0029.1;0.421158,MA0030.1;1.05866,MA0031.1;0.357843,MA0038.1;0.206085,MA0040.1;1.91363,MA0041.1;0.459457,MA0042.1;0.410644,MA0043.1;0.495289,MA0046.1;0.485466,MA0048.1;0.14539,MA0050.1;0.131853,MA0051.1;0.203156,MA0052.1;0.429421,MA0055.1;0.0155313,MA0056.1;0,MA0057.1;0.0582452,MA0058.1;1.02477,MA0059.1;1.02017,MA0060.1;0.0198514,MA0061.1;0.0666801,MA0063.1;0,MA0066.1;0.595133,MA0067.1;0.78548,MA0068.1;0.118488,MA0069.1;0.482095,MA0070.1;0.472333,MA0071.1;0.179775,MA0072.1;0.468422,MA0073.1;0.398218,MA0074.1;0.202636,MA0076.1;0.094817,MA0077.1;0.461731,MA0078.1;0.755792,MA0081.1;1.02075,MA0083.1;0.501617,MA0084.1;0.964138,MA0087.1;0.466297,MA0088.1;0.699285,MA0089.1;0,MA0090.1;0.335123,MA0091.1;0.140889,MA0092.1;0.378282,MA0093.1;0.810084,MA0095.1;0,MA0098.1;0,MA0100.1;0.215803,MA0101.1;0.217713,MA0103.1;1.174,MA0105.1;0.0140394,MA0106.1;0.663531,MA0107.1;0.13479,MA0108.2;0.355343,MA0109.1;0,MA0111.1;0.718751,MA0113.1;0.247415,MA0114.1;0.129654,MA0115.1;0.71383,MA0116.1;0.0344979,MA0117.1;0.528241,MA0119.1;0.0783963,MA0122.1;0.551352,MA0124.1;0.675302,MA0125.1;0.598285,MA0130.1;0,MA0131.1;0.289284,MA0132.1;0,MA0133.1;0,MA0135.1;0.521813,MA0136.1;0.606126,MA0139.1;1.13122,MA0140.1;0.178014,MA0141.1;0.288855,MA0142.1;0.88389,MA0143.1;0.691772,MA0144.1;1.62444,MA0145.1;0.246222,MA0146.1;0.0186319,MA0147.1;0.141953,MA0148.1;0.154621,MA0149.1;0.17166,MA0062.2;0.0131657,MA0035.2;0.525759,MA0039.2;0.0184365,MA0138.2;0.276299,MA0002.2;0.389794,MA0137.2;0.511766,MA0104.2;0.0874345,MA0047.2;0.226642,MA0112.2;0.223605,MA0065.2;0.071155,MA0150.1;0.0992631,MA0151.1;0,MA0152.1;0.182375,MA0153.1;0.583009,MA0154.1;0.107659,MA0155.1;0.112192,MA0156.1;0.240796,MA0157.1;0.310364,MA0158.1;0,MA0159.1;0.944104,MA0160.1;0.493256,MA0161.1;0,MA0162.1;0.00132146,MA0163.1;0.01442,MA0164.1;0.256631,MA0080.2;0.467443,MA0018.2;0.236412,MA0099.2;0.538063,MA0079.2;2.56124e-05,MA0102.2;1.00004,MA0258.1;0.783032,MA0259.1;0.150791,MA0442.1;0
}}
}}

Revision as of 19:09, 22 January 2013


Full id: C419_acute_chronic_thymus_xeroderma_Burkitt_Hodgkin_CD4



Phase1 CAGE Peaks

Hg19::chr10:103666778..103666783,+p@chr10:103666778..103666783
+
Hg19::chr1:158299745..158299756,-p@chr1:158299745..158299756
-
Hg19::chr1:158300194..158300203,-p@chr1:158300194..158300203
-
Hg19::chr1:158323920..158323926,+p23@CD1E
Hg19::chr1:158323949..158323968,+p14@CD1E
Hg19::chr1:158324295..158324300,+p@chr1:158324295..158324300
+
Hg19::chr1:158326285..158326296,+p15@CD1E
Hg19::chr1:158326571..158326578,+p@chr1:158326571..158326578
+
Hg19::chr1:158326653..158326662,+p@chr1:158326653..158326662
+
Hg19::chr1:158326841..158326852,+p@chr1:158326841..158326852
+
Hg19::chr1:158327034..158327044,+p@chr1:158327034..158327044
+
Hg19::chr2:128398152..128398168,-p15@LIMS2
Hg19::chr4:145580883..145580893,+p@chr4:145580883..145580893
+
Hg19::chr4:8204368..8204371,+p@chr4:8204368..8204371
+
Hg19::chr7:142498552..142498565,+p@chr7:142498552..142498565
+
Hg19::chr7:142498640..142498656,+p@chr7:142498640..142498656
+
Hg19::chr7:142498877..142498900,+p2@AJ568018
Hg19::chr7:142498934..142498946,+p3@L34740
Hg19::chr7:142499376..142499383,+p@chr7:142499376..142499383
+
Hg19::chr8:1897606..1897618,-p@chr8:1897606..1897618
-
Hg19::chr8:1900745..1900751,+p@chr8:1900745..1900751
+
Hg19::chr9:100732599..100732614,+p@chr9:100732599..100732614
+
Hg19::chr9:35650561..35650570,-p3@SIT1
Hg19::chr9:35650572..35650659,-p2@SIT1


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:0006955immune response0.00762103817707793
GO:0002376immune system process0.00762103817707793
GO:0044459plasma membrane part0.0223191625900676
GO:0042169SH2 domain binding0.0307081295662209



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
thymus8.36e-344
hemolymphoid system gland8.36e-344
thymic region8.36e-344
pharyngeal gland8.36e-344
thymus primordium8.36e-344
pharyngeal epithelium6.07e-236
hemopoietic organ7.84e-207
immune organ7.84e-207
neck3.25e-1410
gland of gut3.25e-1410
chordate pharynx3.25e-1410
pharyngeal region of foregut3.25e-1410
pharynx5.10e-1311
entire pharyngeal arch endoderm5.10e-1311
early pharyngeal endoderm5.10e-1311
pharyngeal arch system2.42e-0818
upper respiratory tract5.94e-0819


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)
MA0003.10.000121805
MA0004.10.430931
MA0006.10.0576274
MA0007.10.128232
MA0009.10.495012
MA0014.10.00150727
MA0017.10.0747264
MA0019.10.238234
MA0024.10.404839
MA0025.10.614568
MA0027.12.05626
MA0028.10.0643724
MA0029.10.421158
MA0030.11.05866
MA0031.10.357843
MA0038.10.206085
MA0040.11.91363
MA0041.10.459457
MA0042.10.410644
MA0043.10.495289
MA0046.10.485466
MA0048.10.14539
MA0050.10.131853
MA0051.10.203156
MA0052.10.429421
MA0055.10.0155313
MA0056.10
MA0057.10.0582452
MA0058.11.02477
MA0059.11.02017
MA0060.10.0198514
MA0061.10.0666801
MA0063.10
MA0066.10.595133
MA0067.10.78548
MA0068.10.118488
MA0069.10.482095
MA0070.10.472333
MA0071.10.179775
MA0072.10.468422
MA0073.10.398218
MA0074.10.202636
MA0076.10.094817
MA0077.10.461731
MA0078.10.755792
MA0081.11.02075
MA0083.10.501617
MA0084.10.964138
MA0087.10.466297
MA0088.10.699285
MA0089.10
MA0090.10.335123
MA0091.10.140889
MA0092.10.378282
MA0093.10.810084
MA0095.10
MA0098.10
MA0100.10.215803
MA0101.10.217713
MA0103.11.174
MA0105.10.0140394
MA0106.10.663531
MA0107.10.13479
MA0108.20.355343
MA0109.10
MA0111.10.718751
MA0113.10.247415
MA0114.10.129654
MA0115.10.71383
MA0116.10.0344979
MA0117.10.528241
MA0119.10.0783963
MA0122.10.551352
MA0124.10.675302
MA0125.10.598285
MA0130.10
MA0131.10.289284
MA0132.10
MA0133.10
MA0135.10.521813
MA0136.10.606126
MA0139.11.13122
MA0140.10.178014
MA0141.10.288855
MA0142.10.88389
MA0143.10.691772
MA0144.11.62444
MA0145.10.246222
MA0146.10.0186319
MA0147.10.141953
MA0148.10.154621
MA0149.10.17166
MA0062.20.0131657
MA0035.20.525759
MA0039.20.0184365
MA0138.20.276299
MA0002.20.389794
MA0137.20.511766
MA0104.20.0874345
MA0047.20.226642
MA0112.20.223605
MA0065.20.071155
MA0150.10.0992631
MA0151.10
MA0152.10.182375
MA0153.10.583009
MA0154.10.107659
MA0155.10.112192
MA0156.10.240796
MA0157.10.310364
MA0158.10
MA0159.10.944104
MA0160.10.493256
MA0161.10
MA0162.10.00132146
MA0163.10.01442
MA0164.10.256631
MA0080.20.467443
MA0018.20.236412
MA0099.20.538063
MA0079.22.56124e-05
MA0102.21.00004
MA0258.10.783032
MA0259.10.150791
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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