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{{Coexpression_clusters
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4685,0.0022686,0.246105,0.173026,4.57234e-09,0.139785,0.0208458,0.240478,0.156465,0.00899301,0.256963,0.0269005,0.000975743,0.0166394,0.0969345,0.202137,4.34104e-05,0.280943,0.00206803,0.0822373,0.202065,0.000220289,0.0536053,0.00147244,0.15113,0.078016,0.0407233,0.0537355,0.00717361,0.261724,0.00186843,0.187731,0.233626,0.189559,9.53285e-05,0.00497886,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.00298405,0.128736,0.109171,0.000987475,0.066952,0.000128551,0.0367455,0.13497,0.204393,0.295769,0.286691,0.0687209,6.11966e-07,0.263159,0.255956,0.00157056,0.0280973,0.29837,0.253509,0.177664,0.28365,8.95859e-07,0.131761,1.18703e-06,0.206239,8.50764e-05,0.0457735,9.52066e-06,0.325148,0.00698179,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,2.78967e-09,0.249955,0.00084829,0.00225856,0.0935776,0.000754551,0.0276507,0.000101879,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,4.6913e-08,0.000185889,0.00220393,0.175934,0.157274,5.76638e-06,0.00332029,0.205954,0.000104314|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,1.54806,0.853988,0.937929,0.494933,1.23181,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.718382,0.63803,0.151453,0.726632,0.939121,0.808003,1.28131,0.645308,1.02504,0.951993,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,2.67708,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,1.81344,1.12884,1.20029,0.73687,1.16162,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,1.76229,1.053,2.0169,1.63834,1.36973,1.23218,1.34254,0.642354,1.37703,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,3.53119,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.974093,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,2.94727,0.710709,1.56892,1.35169,4.35547,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232|tfbs_overrepresentation_jaspar=MA0003.1;0.0471418,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.118426,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;2.16573,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.557638,MA0056.1;0,MA0057.1;1.59304,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.0185922,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;2.63873,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;2.34614,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;1.31729,MA0145.1;0.273764,MA0146.1;0.107247,MA0147.1;0.565108,MA0148.1;3.29283,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.0526989,MA0138.2;1.04628,MA0002.2;1.20011,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;2.23118,MA0112.2;0.264678,MA0065.2;0.760954,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;4.15415,MA0155.1;0.256269,MA0156.1;1.60572,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.00160703,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4570_placenta_hippocampus_pons_amygdala_occipital_medulla_cerebellum
|id=C4570
}}

Latest revision as of 14:15, 17 September 2013


Full id: C4570_placenta_hippocampus_pons_amygdala_occipital_medulla_cerebellum



Phase1 CAGE Peaks

Hg19::chr6:143929225..143929246,+p9@PHACTR2
Hg19::chr6:143929307..143929322,+p4@PHACTR2
Hg19::chr6:143929329..143929340,+p13@PHACTR2


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube1.28e-9056
neural rod1.28e-9056
future spinal cord1.28e-9056
neural keel1.28e-9056
regional part of nervous system1.69e-8653
regional part of brain1.69e-8653
regional part of forebrain1.93e-6941
forebrain1.93e-6941
anterior neural tube1.93e-6941
future forebrain1.93e-6941
telencephalon1.35e-6834
brain grey matter2.03e-6834
gray matter2.03e-6834
brain2.59e-6868
future brain2.59e-6868
cerebral hemisphere6.46e-6832
central nervous system7.17e-6681
regional part of cerebral cortex2.43e-6522
regional part of telencephalon1.83e-6232
neural plate4.12e-5982
presumptive neural plate4.12e-5982
nervous system2.02e-5889
neocortex2.83e-5820
cerebral cortex3.91e-5725
pallium3.91e-5725
neurectoderm6.18e-5686
adult organism1.78e-52114
ecto-epithelium1.22e-44104
pre-chordal neural plate1.87e-4461
structure with developmental contribution from neural crest3.53e-37132
ectoderm-derived structure4.67e-26171
ectoderm4.67e-26171
presumptive ectoderm4.67e-26171
gyrus2.54e-216
organ system subdivision3.22e-21223
posterior neural tube3.37e-2115
chordal neural plate3.37e-2115
tube5.12e-21192
limbic system5.41e-195
temporal lobe1.67e-186
parietal lobe8.07e-185
segmental subdivision of hindbrain1.94e-1712
hindbrain1.94e-1712
presumptive hindbrain1.94e-1712
segmental subdivision of nervous system5.43e-1613
anatomical conduit7.29e-16240
brainstem1.42e-146
basal ganglion1.08e-139
nuclear complex of neuraxis1.08e-139
aggregate regional part of brain1.08e-139
collection of basal ganglia1.08e-139
cerebral subcortex1.08e-139
regional part of metencephalon1.76e-139
metencephalon1.76e-139
future metencephalon1.76e-139
organ part3.66e-13218
neural nucleus4.69e-139
nucleus of brain4.69e-139
occipital lobe4.53e-125
frontal cortex1.12e-113
pons3.01e-113
epithelium4.25e-11306
cell layer6.79e-11309
anatomical cluster2.90e-09373
multi-tissue structure6.54e-09342
amygdala9.94e-092
Ammon's horn9.94e-092
lobe parts of cerebral cortex9.94e-092
hippocampal formation9.94e-092
limbic lobe9.94e-092
corpus striatum1.85e-084
striatum1.85e-084
ventral part of telencephalon1.85e-084
future corpus striatum1.85e-084
middle temporal gyrus2.96e-082
middle frontal gyrus3.07e-082
telencephalic nucleus5.74e-087
organ6.70e-08503
dorsal plus ventral thalamus1.04e-072
locus ceruleus1.04e-072
brainstem nucleus1.04e-072
hindbrain nucleus1.04e-072
thalamic complex1.04e-072


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.12.16573
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.12.63873
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.12.34614
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.11.31729
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.13.29283
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.22.23118
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.14.15415
MA0155.10.256269
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.00160703
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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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