Coexpression cluster:C4448: Difference between revisions
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Latest revision as of 12:46, 17 September 2013
Full id: C4448_Neutrophils_pons_brain_frontal_Eosinophils_Mast_spinal
Phase1 CAGE Peaks
| Hg19::chr5:108745603..108745631,- | p1@PJA2 |
| Hg19::chr6:122792919..122792970,- | p1@SERINC1 |
| Hg19::chr6:122792978..122792992,- | p2@SERINC1 |
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 ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0032329 | serine transport | 0.00238428140252734 |
| GO:0015825 | L-serine transport | 0.00238428140252734 |
| GO:0022889 | serine transmembrane transporter activity | 0.00238428140252734 |
| GO:0015194 | L-serine transmembrane transporter activity | 0.00238428140252734 |
| GO:0005789 | endoplasmic reticulum membrane | 0.0025456993930067 |
| GO:0042175 | nuclear envelope-endoplasmic reticulum network | 0.0025456993930067 |
| GO:0044432 | endoplasmic reticulum part | 0.00270600274992411 |
| GO:0006658 | phosphatidylserine metabolic process | 0.00476814168412872 |
| GO:0015807 | L-amino acid transport | 0.00529777923387416 |
| GO:0005783 | endoplasmic reticulum | 0.00575482801364196 |
| GO:0015804 | neutral amino acid transport | 0.00617501311531734 |
| GO:0012505 | endomembrane system | 0.00617501311531734 |
| GO:0015175 | neutral amino acid transmembrane transporter activity | 0.00623443615742896 |
| GO:0015179 | L-amino acid transmembrane transporter activity | 0.0106759301763204 |
| GO:0031090 | organelle membrane | 0.0106759301763204 |
| GO:0015171 | amino acid transmembrane transporter activity | 0.0185258503936613 |
| GO:0006665 | sphingolipid metabolic process | 0.0185258503936613 |
| GO:0006865 | amino acid transport | 0.0185258503936613 |
| GO:0015837 | amine transport | 0.0200384602203091 |
| GO:0046943 | carboxylic acid transmembrane transporter activity | 0.0200384602203091 |
| GO:0046942 | carboxylic acid transport | 0.0200384602203091 |
| GO:0015849 | organic acid transport | 0.0200384602203091 |
| GO:0005342 | organic acid transmembrane transporter activity | 0.0200384602203091 |
| GO:0006650 | glycerophospholipid metabolic process | 0.0200384602203091 |
| GO:0051347 | positive regulation of transferase activity | 0.027268406000498 |
| GO:0045211 | postsynaptic membrane | 0.027268406000498 |
| GO:0044456 | synapse part | 0.0283682184882672 |
| GO:0005886 | plasma membrane | 0.0352423033661863 |
| GO:0006644 | phospholipid metabolic process | 0.0352423033661863 |
| GO:0051338 | regulation of transferase activity | 0.0368541894013872 |
| GO:0044446 | intracellular organelle part | 0.0368541894013872 |
| GO:0044422 | organelle part | 0.0368541894013872 |
| GO:0043085 | positive regulation of catalytic activity | 0.0368541894013872 |
| GO:0006643 | membrane lipid metabolic process | 0.0379968989070936 |
| GO:0044444 | cytoplasmic part | 0.0422762736071943 |
| GO:0000139 | Golgi membrane | 0.0480896116943764 |
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>
| Ontology term | p-value | n |
|---|---|---|
| myeloid leukocyte | 2.35e-10 | 72 |
| myeloid lineage restricted progenitor cell | 7.37e-09 | 66 |
| granulocyte monocyte progenitor cell | 2.37e-07 | 67 |
| monopoietic cell | 4.94e-07 | 59 |
| monocyte | 4.94e-07 | 59 |
| monoblast | 4.94e-07 | 59 |
| promonocyte | 4.94e-07 | 59 |
| macrophage dendritic cell progenitor | 9.36e-07 | 61 |
| Ontology term | p-value | n |
|---|---|---|
| adult organism | 1.43e-34 | 114 |
| neural tube | 6.52e-23 | 56 |
| neural rod | 6.52e-23 | 56 |
| future spinal cord | 6.52e-23 | 56 |
| neural keel | 6.52e-23 | 56 |
| regional part of nervous system | 8.70e-22 | 53 |
| regional part of brain | 8.70e-22 | 53 |
| central nervous system | 1.03e-20 | 81 |
| regional part of forebrain | 1.30e-20 | 41 |
| forebrain | 1.30e-20 | 41 |
| anterior neural tube | 1.30e-20 | 41 |
| future forebrain | 1.30e-20 | 41 |
| brain | 1.19e-19 | 68 |
| future brain | 1.19e-19 | 68 |
| nervous system | 1.29e-18 | 89 |
| telencephalon | 6.54e-17 | 34 |
| brain grey matter | 8.61e-17 | 34 |
| gray matter | 8.61e-17 | 34 |
| cerebral hemisphere | 9.10e-16 | 32 |
| regional part of telencephalon | 1.11e-15 | 32 |
| neural plate | 5.78e-14 | 82 |
| presumptive neural plate | 5.78e-14 | 82 |
| regional part of cerebral cortex | 1.67e-13 | 22 |
| neurectoderm | 5.74e-13 | 86 |
| neocortex | 2.25e-12 | 20 |
| cerebral cortex | 7.40e-12 | 25 |
| pallium | 7.40e-12 | 25 |
| pre-chordal neural plate | 3.16e-11 | 61 |
| structure with developmental contribution from neural crest | 1.15e-10 | 132 |
| ectoderm-derived structure | 1.98e-09 | 171 |
| ectoderm | 1.98e-09 | 171 |
| presumptive ectoderm | 1.98e-09 | 171 |
| ecto-epithelium | 2.00e-09 | 104 |
| organ | 5.80e-08 | 503 |
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) |
|---|---|
| MA0003.1 | 0.0471418 |
| MA0004.1 | 0.826076 |
| MA0006.1 | 0.639288 |
| MA0007.1 | 0.804807 |
| MA0009.1 | 1.3275 |
| MA0014.1 | 0.377374 |
| MA0017.1 | 0.686276 |
| MA0019.1 | 0.990656 |
| MA0024.1 | 1.21731 |
| MA0025.1 | 1.46617 |
| MA0027.1 | 2.95767 |
| MA0028.1 | 1.58389 |
| MA0029.1 | 1.23771 |
| MA0030.1 | 1.22561 |
| MA0031.1 | 1.15713 |
| MA0038.1 | 0.94098 |
| 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 | 0.190716 |
| MA0056.1 | 0 |
| MA0057.1 | 0.333427 |
| 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 | 0.0834661 |
| MA0074.1 | 0.935474 |
| MA0076.1 | 1.74184 |
| 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 | 0.646932 |
| MA0103.1 | 0.628063 |
| MA0105.1 | 0.31555 |
| MA0106.1 | 0.986396 |
| MA0107.1 | 0.556367 |
| 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 | 2.18164 |
| 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 | 1.16674 |
| MA0147.1 | 0.565108 |
| MA0148.1 | 0.854239 |
| MA0149.1 | 0.884158 |
| MA0062.2 | 1.9924 |
| MA0035.2 | 0.894194 |
| MA0039.2 | 0.432958 |
| MA0138.2 | 1.04628 |
| MA0002.2 | 0.476938 |
| MA0137.2 | 0.666381 |
| MA0104.2 | 0.491226 |
| MA0047.2 | 0.973066 |
| MA0112.2 | 0.731309 |
| MA0065.2 | 0.277623 |
| MA0150.1 | 0.744617 |
| MA0151.1 | 0 |
| MA0152.1 | 0.902317 |
| MA0153.1 | 1.43021 |
| MA0154.1 | 0.312019 |
| 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 | 1.43223 |
| MA0163.1 | 0.122425 |
| MA0164.1 | 1.01792 |
| MA0080.2 | 1.55139 |
| MA0018.2 | 0.987913 |
| MA0099.2 | 0.902716 |
| MA0079.2 | 0.311277 |
| MA0102.2 | 1.88331 |
| MA0258.1 | 0.519674 |
| MA0259.1 | 0.575594 |
| MA0442.1 | 0 |
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 | #promoters | Enrichment | p-value | q-value |
|---|---|---|---|---|
| E2F1#1869 | 3 | 4.90738921487932 | 0.00846098534723939 | 0.0327001757273558 |
| ELF1#1997 | 3 | 4.25809795880754 | 0.0129517987505461 | 0.0464277641911201 |
| GABPB1#2553 | 3 | 7.06768383618217 | 0.00283221282541742 | 0.0154630913938925 |
| IRF1#3659 | 3 | 7.6371637535639 | 0.00224469274729724 | 0.0128576463464584 |
| RFX5#5993 | 3 | 12.0479108271951 | 0.000571724605031258 | 0.00486003141989741 |
| SIN3A#25942 | 3 | 5.40888472681514 | 0.00631896197799152 | 0.0277872029481876 |
| SP1#6667 | 3 | 5.6983813781409 | 0.00540396270171217 | 0.0247558759805297 |
| TRIM28#10155 | 2 | 12.3936833635083 | 0.00836834412943847 | 0.0329381733826194 |
| YY1#7528 | 3 | 4.91117074985386 | 0.00844145534180826 | 0.0330726321207605 |
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.
