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Coexpression cluster:C1329: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.756372,MA0004.1;1.37419,MA0006.1;1.79433,MA0007.1;1.33289,MA0009.1;1.03681,MA0014.1;1.56589,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;0.906394,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.213007,MA0056.1;0,MA0057.1;0.882847,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;1.24837,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;1.87192,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;1.09824,MA0089.1;0,MA0090.1;0.490736,MA0091.1;1.37996,MA0092.1;0.522012,MA0093.1;1.02138,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.830067,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;1.52717,MA0115.1;1.28169,MA0116.1;6.38679,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;1.19942,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.811435,MA0145.1;0.347815,MA0146.1;0.232472,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.0929059,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;1.06611,MA0104.2;0.735746,MA0047.2;0.695777,MA0112.2;0.332548,MA0065.2;1.18263,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;2.59196,MA0155.1;1.60937,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;1.87239,MA0163.1;2.08316,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;6.06794,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.893594,MA0442.1;0
}}
}}

Revision as of 19:51, 22 January 2013


Full id: C1329_aorta_retina_uterus_smooth_gall_heart_diaphragm



Phase1 CAGE Peaks

Hg19::chr11:10715033..10715105,-p1@MRVI1
Hg19::chr19:38743940..38743957,-p@chr19:38743940..38743957
-
Hg19::chr19:38743966..38743977,-p@chr19:38743966..38743977
-
Hg19::chr6:168841817..168841848,+p2@SMOC2
Hg19::chr6:168841853..168841874,+p1@SMOC2
Hg19::chr6:168841898..168841909,+p3@SMOC2


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:0016528sarcoplasm0.0213335658544728
GO:0016529sarcoplasmic reticulum0.0213335658544728



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
fat cell7.12e-0915
Uber Anatomy
Ontology termp-valuen
adult organism1.34e-67114
neural tube1.48e-2556
neural rod1.48e-2556
future spinal cord1.48e-2556
neural keel1.48e-2556
regional part of nervous system9.33e-2553
regional part of brain9.33e-2553
central nervous system6.32e-2081
regional part of forebrain7.70e-2041
forebrain7.70e-2041
anterior neural tube7.70e-2041
future forebrain7.70e-2041
nervous system6.60e-1989
brain1.22e-1868
future brain1.22e-1868
neural plate3.52e-1882
presumptive neural plate3.52e-1882
neurectoderm2.07e-1786
organ system subdivision4.59e-16223
telencephalon8.62e-1634
brain grey matter9.07e-1634
gray matter9.07e-1634
regional part of telencephalon1.49e-1432
cerebral hemisphere1.67e-1432
structure with developmental contribution from neural crest1.32e-13132
pre-chordal neural plate6.58e-1261
ecto-epithelium7.27e-12104
neocortex2.75e-1120
regional part of cerebral cortex4.11e-1122
anatomical cluster2.17e-10373
cerebral cortex3.98e-1025
pallium3.98e-1025
multi-cellular organism6.32e-09656
organ part7.31e-09218
organ1.57e-08503
ectoderm-derived structure2.23e-08171
ectoderm2.23e-08171
presumptive ectoderm2.23e-08171
multi-tissue structure2.42e-08342
neural nucleus1.64e-079
nucleus of brain1.64e-079
basal ganglion2.24e-079
nuclear complex of neuraxis2.24e-079
aggregate regional part of brain2.24e-079
collection of basal ganglia2.24e-079
cerebral subcortex2.24e-079
tube3.40e-07192
anatomical conduit4.35e-07240
segmental subdivision of nervous system5.39e-0713
posterior neural tube6.10e-0715
chordal neural plate6.10e-0715
gastrointestinal system9.67e-0725


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)
MA0003.10.756372
MA0004.11.37419
MA0006.11.79433
MA0007.11.33289
MA0009.11.03681
MA0014.11.56589
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.906394
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.213007
MA0056.10
MA0057.10.882847
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.11.24837
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.11.87192
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.09824
MA0089.10
MA0090.10.490736
MA0091.11.37996
MA0092.10.522012
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.830067
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.11.52717
MA0115.11.28169
MA0116.16.38679
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.11.19942
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.811435
MA0145.10.347815
MA0146.10.232472
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.0929059
MA0138.20.765223
MA0002.20.255126
MA0137.21.06611
MA0104.20.735746
MA0047.20.695777
MA0112.20.332548
MA0065.21.18263
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.12.59196
MA0155.11.60937
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.11.87239
MA0163.12.08316
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.26.06794
MA0102.21.58513
MA0258.10.289793
MA0259.10.893594
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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