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{{Coexpression_clusters
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|full_id=C4470_Chondrocyte_substantia_globus_kidney_spinal_diencephalon_medulla
|id=C4470
|ontology_enrichment_celltype=CL:0000327!2.40e-07!14
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!5.76e-59!115;UBERON:0001049!8.15e-37!57;UBERON:0005068!8.15e-37!57;UBERON:0006241!8.15e-37!57;UBERON:0007135!8.15e-37!57;UBERON:0002616!2.54e-32!59;UBERON:0003080!3.95e-29!42;UBERON:0002780!2.03e-28!41;UBERON:0001890!2.03e-28!41;UBERON:0006240!2.03e-28!41;UBERON:0001017!3.26e-28!82;UBERON:0000955!1.28e-27!69;UBERON:0006238!1.28e-27!69;UBERON:0005743!4.77e-27!86;UBERON:0000073!2.93e-25!94;UBERON:0001016!2.93e-25!94;UBERON:0002020!6.35e-25!34;UBERON:0003528!6.35e-25!34;UBERON:0001893!9.48e-25!34;UBERON:0002346!1.81e-24!90;UBERON:0003075!3.58e-24!86;UBERON:0007284!3.58e-24!86;UBERON:0002791!6.74e-24!33;UBERON:0001869!7.57e-23!32;UBERON:0002619!2.48e-17!22;UBERON:0000956!1.18e-16!25;UBERON:0000203!1.18e-16!25;UBERON:0003056!3.05e-16!61;UBERON:0000153!9.20e-16!129;UBERON:0007811!9.20e-16!129;UBERON:0001950!1.33e-15!20;UBERON:0000033!8.53e-15!123;UBERON:0000924!2.41e-12!173;UBERON:0006601!2.41e-12!173;UBERON:0004121!6.57e-12!169;UBERON:0002308!5.57e-10!9;UBERON:0000125!5.57e-10!9;UBERON:0002420!6.94e-10!9;UBERON:0007245!6.94e-10!9;UBERON:0010009!6.94e-10!9;UBERON:0010011!6.94e-10!9;UBERON:0000454!6.94e-10!9;UBERON:0000025!5.72e-09!194;UBERON:0002298!5.73e-09!8;UBERON:0000475!5.90e-09!365;UBERON:0003076!8.55e-09!15;UBERON:0003057!8.55e-09!15;UBERON:0004111!2.80e-08!241;UBERON:0009663!4.74e-08!7;UBERON:0000477!2.44e-07!286;UBERON:0004732!4.78e-07!13
}}

Latest revision as of 12:46, 17 September 2013


Full id: C4470_Chondrocyte_substantia_globus_kidney_spinal_diencephalon_medulla



Phase1 CAGE Peaks

Hg19::chr5:142077232..142077314,-p5@FGF1
Hg19::chr5:142077559..142077566,-p9@FGF1
Hg19::chr5:142077569..142077596,-p3@FGF1


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
collagen secreting cell1.09e-076
chondroblast1.09e-076
chondrocyte1.09e-076
GAG secreting cell8.18e-079
carbohydrate secreting cell8.18e-079
Uber Anatomy
Ontology termp-valuen
adult organism2.16e-78114
neural tube7.70e-4456
neural rod7.70e-4456
future spinal cord7.70e-4456
neural keel7.70e-4456
regional part of nervous system9.82e-4053
regional part of brain9.82e-4053
central nervous system1.09e-3281
brain3.88e-3268
future brain3.88e-3268
neural plate1.70e-3182
presumptive neural plate1.70e-3182
regional part of forebrain3.57e-3141
forebrain3.57e-3141
anterior neural tube3.57e-3141
future forebrain3.57e-3141
brain grey matter2.28e-2934
gray matter2.28e-2934
neurectoderm2.72e-2986
nervous system3.52e-2989
telencephalon4.23e-2934
regional part of telencephalon1.58e-2632
cerebral hemisphere2.55e-2632
structure with developmental contribution from neural crest2.07e-24132
ecto-epithelium1.06e-22104
regional part of cerebral cortex2.03e-2022
pre-chordal neural plate6.62e-1961
neocortex6.23e-1820
cerebral cortex2.41e-1725
pallium2.41e-1725
organ system subdivision9.85e-15223
neural nucleus1.33e-149
nucleus of brain1.33e-149
basal ganglion1.84e-149
nuclear complex of neuraxis1.84e-149
aggregate regional part of brain1.84e-149
collection of basal ganglia1.84e-149
cerebral subcortex1.84e-149
ectoderm-derived structure1.84e-14171
ectoderm1.84e-14171
presumptive ectoderm1.84e-14171
posterior neural tube1.62e-1315
chordal neural plate1.62e-1315
tube6.54e-12192
telencephalic nucleus1.33e-117
brainstem1.87e-106
anatomical conduit7.54e-10240
segmental subdivision of hindbrain1.30e-0912
hindbrain1.30e-0912
presumptive hindbrain1.30e-0912
gyrus2.12e-096
anatomical cluster4.70e-09373
organ part4.97e-09218
multi-tissue structure1.02e-08342
segmental subdivision of nervous system1.06e-0813
limbic system1.60e-085
cell layer3.22e-08309
organ9.76e-08503
epithelium1.06e-07306
corpus striatum4.57e-074
striatum4.57e-074
ventral part of telencephalon4.57e-074
future corpus striatum4.57e-074


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)
MA0003.10.178364
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
MA0038.10.94098
MA0040.11.24388
MA0041.11.97353
MA0042.11.89908
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.12.1667
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.407479
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
MA0101.10.646932
MA0103.11.52002
MA0105.10.31555
MA0106.10.986396
MA0107.11.36919
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
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
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
MA0079.20.0107199
MA0102.21.88331
MA0258.11.29138
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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