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Coexpression cluster:C1921: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.481059,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;3.07977,MA0017.1;2.14806,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;2.0635,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;0.195817,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;4.0988,MA0056.1;0,MA0057.1;0.554727,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;1.44118,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;1.98392,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.111822,MA0074.1;0.730989,MA0076.1;2.29573,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.132006,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;1.16366,MA0103.1;0.442769,MA0105.1;0.520776,MA0106.1;0.779931,MA0107.1;0.985964,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;3.87914,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.143698,MA0146.1;1.35428,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;2.17426,MA0035.2;0.691506,MA0039.2;0.527987,MA0138.2;0.837782,MA0002.2;0.83106,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.839774,MA0065.2;1.41695,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;2.24205,MA0155.1;0.409315,MA0156.1;2.09554,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;1.72541,MA0163.1;1.49262,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;2.44686,MA0102.2;1.66336,MA0258.1;2.47453,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:17, 22 January 2013


Full id: C1921_small_Renal_Ciliary_Astrocyte_Lens_Meningeal_maxillary



Phase1 CAGE Peaks

Hg19::chr3:139258363..139258374,-p4@RBP1
Hg19::chr3:139258382..139258393,-p5@RBP1
Hg19::chr3:139258420..139258434,-p3@RBP1
Hg19::chr3:139258443..139258485,-p1@RBP1
Hg19::chr3:139258521..139258589,-p2@RBP1


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

No GOStat results

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
embryonic cell1.71e-12250
epithelial cell of nephron3.87e-0815
contractile cell3.09e-0759
electrically responsive cell6.35e-0761
electrically active cell6.35e-0761
Uber Anatomy
Ontology termp-valuen
anatomical cluster4.66e-40373
multi-tissue structure2.59e-34342
cell layer1.98e-31309
epithelium2.39e-30306
anatomical conduit7.51e-27240
embryo5.75e-24592
organ system subdivision2.29e-23223
tube1.04e-22192
multi-cellular organism4.25e-22656
developing anatomical structure4.70e-21581
ectoderm-derived structure2.63e-20171
ectoderm2.63e-20171
presumptive ectoderm2.63e-20171
neurectoderm4.80e-2086
neural plate5.52e-2082
presumptive neural plate5.52e-2082
anatomical system6.75e-20624
anatomical group1.29e-19625
embryonic structure2.84e-19564
central nervous system2.46e-1881
structure with developmental contribution from neural crest3.17e-18132
germ layer7.39e-18560
germ layer / neural crest7.39e-18560
embryonic tissue7.39e-18560
presumptive structure7.39e-18560
germ layer / neural crest derived structure7.39e-18560
epiblast (generic)7.39e-18560
nervous system3.08e-1789
ecto-epithelium3.95e-17104
organism subdivision2.64e-16264
organ1.34e-15503
brain3.44e-1568
future brain3.44e-1568
organ part3.54e-14218
pre-chordal neural plate3.75e-1461
mesenchyme2.67e-13160
entire embryonic mesenchyme2.67e-13160
neural tube1.04e-1256
neural rod1.04e-1256
future spinal cord1.04e-1256
neural keel1.04e-1256
primordium3.38e-12160
regional part of nervous system6.16e-1253
regional part of brain6.16e-1253
immaterial anatomical entity2.26e-11117
epithelial tube2.59e-11117
trunk mesenchyme3.92e-11122
adult organism3.33e-10114
compound organ4.54e-1068
trunk region element1.97e-09101
trunk4.23e-09199
sense organ6.32e-0924
sensory system6.32e-0924
entire sense organ system6.32e-0924
excretory tube2.34e-0816
kidney epithelium2.34e-0816
regional part of forebrain3.41e-0841
forebrain3.41e-0841
anterior neural tube3.41e-0841
future forebrain3.41e-0841
nephron epithelium3.87e-0815
renal tubule3.87e-0815
nephron tubule3.87e-0815
nephron3.87e-0815
uriniferous tubule3.87e-0815
nephrogenic mesenchyme3.87e-0815
anatomical space4.00e-0895
eye4.82e-0821
visual system4.82e-0821
camera-type eye1.49e-0720
simple eye1.49e-0720
immature eye1.49e-0720
ocular region1.49e-0720
eyeball of camera-type eye1.49e-0720
optic cup1.49e-0720
optic vesicle1.49e-0720
eye primordium1.49e-0720
parenchyma1.54e-0715
head2.08e-0756
abdomen element2.11e-0754
abdominal segment element2.11e-0754
face2.80e-0722
pigment epithelium of eye4.70e-0711
anterior region of body9.76e-0762
craniocervical region9.76e-0762


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)
MA0003.10.481059
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.13.07977
MA0017.12.14806
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.12.0635
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
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.14.0988
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.11.44118
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.11.98392
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.111822
MA0074.10.730989
MA0076.12.29573
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.11.16366
MA0103.10.442769
MA0105.10.520776
MA0106.10.779931
MA0107.10.985964
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
MA0139.13.87914
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.11.35428
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.22.17426
MA0035.20.691506
MA0039.20.527987
MA0138.20.837782
MA0002.20.83106
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.839774
MA0065.21.41695
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.12.24205
MA0155.10.409315
MA0156.12.09554
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.11.72541
MA0163.11.49262
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.22.44686
MA0102.21.66336
MA0258.12.47453
MA0259.10.395396
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
E2F1#186954.907389214879320.0003512818099256460.0035337623720694
EBF1#187935.34388010794140.01187615563868110.0432443281064159
TAF1#687253.343046285745290.002394600090870310.0135498531121203
TBP#690853.706770687096390.001428755106721120.00919848074163773
YY1#752854.911170749853860.00034993140821360.00352969734811861



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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