Coexpression cluster:C1390: Difference between revisions
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Latest revision as of 11:43, 17 September 2013
Full id: C1390_Mast_CD8_Natural_Basophils_CD34_CD4_CD19
Phase1 CAGE Peaks
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:0007253 | cytoplasmic sequestering of NF-kappaB | 0.0120973193800372 |
GO:0042347 | negative regulation of NF-kappaB import into nucleus | 0.0120973193800372 |
GO:0000242 | pericentriolar material | 0.0120973193800372 |
GO:0042994 | cytoplasmic sequestering of transcription factor | 0.0120973193800372 |
GO:0051220 | cytoplasmic sequestering of protein | 0.0120973193800372 |
GO:0042308 | negative regulation of protein import into nucleus | 0.0120973193800372 |
GO:0042992 | negative regulation of transcription factor import into nucleus | 0.0120973193800372 |
GO:0042345 | regulation of NF-kappaB import into nucleus | 0.0120973193800372 |
GO:0042348 | NF-kappaB import into nucleus | 0.0120973193800372 |
GO:0046823 | negative regulation of nucleocytoplasmic transport | 0.0120973193800372 |
GO:0051224 | negative regulation of protein transport | 0.0120973193800372 |
GO:0030159 | receptor signaling complex scaffold activity | 0.0120973193800372 |
GO:0032947 | protein complex scaffold | 0.0120973193800372 |
GO:0042990 | regulation of transcription factor import into nucleus | 0.0120973193800372 |
GO:0042991 | transcription factor import into nucleus | 0.0120973193800372 |
GO:0033157 | regulation of intracellular protein transport | 0.0120973193800372 |
GO:0042306 | regulation of protein import into nucleus | 0.0120973193800372 |
GO:0044450 | microtubule organizing center part | 0.0120973193800372 |
GO:0032507 | maintenance of cellular protein localization | 0.0120973193800372 |
GO:0051651 | maintenance of cellular localization | 0.0120973193800372 |
GO:0032386 | regulation of intracellular transport | 0.0120973193800372 |
GO:0045185 | maintenance of protein localization | 0.0120973193800372 |
GO:0051223 | regulation of protein transport | 0.012367641059904 |
GO:0046822 | regulation of nucleocytoplasmic transport | 0.012367641059904 |
GO:0051051 | negative regulation of transport | 0.0126910111404423 |
GO:0048523 | negative regulation of cellular process | 0.0146464428917892 |
GO:0048519 | negative regulation of biological process | 0.0149820926239023 |
GO:0051235 | maintenance of localization | 0.0149820926239023 |
GO:0051028 | mRNA transport | 0.0284818448587953 |
GO:0050658 | RNA transport | 0.0284818448587953 |
GO:0051236 | establishment of RNA localization | 0.0284818448587953 |
GO:0050657 | nucleic acid transport | 0.0284818448587953 |
GO:0006403 | RNA localization | 0.0284818448587953 |
GO:0006606 | protein import into nucleus | 0.0286006223338466 |
GO:0051170 | nuclear import | 0.0286006223338466 |
GO:0015931 | nucleobase, nucleoside, nucleotide and nucleic acid transport | 0.0295033620528052 |
GO:0003714 | transcription corepressor activity | 0.0295314200752571 |
GO:0051049 | regulation of transport | 0.0295578589690544 |
GO:0017038 | protein import | 0.0319304854904982 |
GO:0000122 | negative regulation of transcription from RNA polymerase II promoter | 0.032108983109937 |
GO:0005813 | centrosome | 0.032108983109937 |
GO:0007249 | I-kappaB kinase/NF-kappaB cascade | 0.0337643347359911 |
GO:0005815 | microtubule organizing center | 0.0348689724031423 |
GO:0006913 | nucleocytoplasmic transport | 0.0353498133259162 |
GO:0051169 | nuclear transport | 0.0353498133259162 |
GO:0045892 | negative regulation of transcription, DNA-dependent | 0.0449377503640029 |
GO:0005515 | protein binding | 0.0452836447329336 |
GO:0016564 | transcription repressor activity | 0.0452836447329336 |
GO:0006605 | protein targeting | 0.0452836447329336 |
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 |
---|---|---|
hematopoietic stem cell | 1.47e-29 | 168 |
angioblastic mesenchymal cell | 1.47e-29 | 168 |
hematopoietic cell | 7.74e-28 | 177 |
leukocyte | 9.25e-28 | 136 |
hematopoietic oligopotent progenitor cell | 6.55e-26 | 161 |
hematopoietic multipotent progenitor cell | 6.55e-26 | 161 |
hematopoietic lineage restricted progenitor cell | 3.96e-22 | 120 |
nongranular leukocyte | 8.16e-21 | 115 |
mesenchymal cell | 1.58e-13 | 354 |
lymphocyte | 2.30e-13 | 53 |
common lymphoid progenitor | 2.30e-13 | 53 |
connective tissue cell | 4.93e-13 | 361 |
lymphoid lineage restricted progenitor cell | 5.53e-13 | 52 |
nucleate cell | 6.01e-13 | 55 |
myeloid cell | 6.83e-13 | 108 |
common myeloid progenitor | 6.83e-13 | 108 |
motile cell | 9.39e-12 | 386 |
myeloid leukocyte | 9.74e-11 | 72 |
granulocyte monocyte progenitor cell | 5.11e-10 | 67 |
stem cell | 8.73e-10 | 441 |
multi fate stem cell | 2.68e-09 | 427 |
myeloid lineage restricted progenitor cell | 5.27e-09 | 66 |
somatic stem cell | 1.47e-08 | 433 |
T cell | 4.63e-08 | 25 |
pro-T cell | 4.63e-08 | 25 |
macrophage dendritic cell progenitor | 4.76e-08 | 61 |
monopoietic cell | 3.30e-07 | 59 |
monocyte | 3.30e-07 | 59 |
monoblast | 3.30e-07 | 59 |
promonocyte | 3.30e-07 | 59 |
Ontology term | p-value | n |
---|---|---|
hematopoietic system | 2.63e-15 | 98 |
blood island | 2.63e-15 | 98 |
hemolymphoid system | 2.80e-12 | 108 |
connective tissue | 7.75e-12 | 371 |
blood | 4.04e-09 | 15 |
haemolymphatic fluid | 4.04e-09 | 15 |
organism substance | 4.04e-09 | 15 |
bone marrow | 7.29e-08 | 76 |
immune system | 4.06e-07 | 93 |
bone element | 6.83e-07 | 82 |
skeletal system | 9.30e-07 | 100 |
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 | 0.515118 |
MA0004.1 | 0.558729 |
MA0006.1 | 0.391183 |
MA0007.1 | 0.539222 |
MA0009.1 | 1.03681 |
MA0014.1 | 0.0254709 |
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 | 0.465994 |
MA0056.1 | 0 |
MA0057.1 | 0.147053 |
MA0058.1 | 0.458909 |
MA0059.1 | 2.99917 |
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 | 0.0569999 |
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 | 0.0971959 |
MA0089.1 | 0 |
MA0090.1 | 0.490736 |
MA0091.1 | 1.37996 |
MA0092.1 | 0.522012 |
MA0093.1 | 0.394379 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 1.62836 |
MA0101.1 | 0.397846 |
MA0103.1 | 0.381434 |
MA0105.1 | 1.34409 |
MA0106.1 | 0.70837 |
MA0107.1 | 0.857383 |
MA0108.2 | 0.868347 |
MA0109.1 | 0 |
MA0111.1 | 0.504913 |
MA0113.1 | 0.725375 |
MA0114.1 | 0.314898 |
MA0115.1 | 1.28169 |
MA0116.1 | 0.323925 |
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 | 1.84113 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 1.06778 |
MA0136.1 | 0.672893 |
MA0139.1 | 0.226048 |
MA0140.1 | 0.622527 |
MA0141.1 | 0.455728 |
MA0142.1 | 0.838805 |
MA0143.1 | 0.725558 |
MA0144.1 | 0.299851 |
MA0145.1 | 0.107156 |
MA0146.1 | 0.232472 |
MA0147.1 | 0.87383 |
MA0148.1 | 0.584698 |
MA0149.1 | 0.612449 |
MA0062.2 | 0.658749 |
MA0035.2 | 0.621793 |
MA0039.2 | 0.35955 |
MA0138.2 | 0.765223 |
MA0002.2 | 0.255126 |
MA0137.2 | 0.414885 |
MA0104.2 | 1.35181 |
MA0047.2 | 0.695777 |
MA0112.2 | 0.680553 |
MA0065.2 | 0.109623 |
MA0150.1 | 0.484557 |
MA0151.1 | 0 |
MA0152.1 | 0.629368 |
MA0153.1 | 1.13732 |
MA0154.1 | 0.819655 |
MA0155.1 | 0.65596 |
MA0156.1 | 0.417278 |
MA0157.1 | 0.810597 |
MA0158.1 | 0 |
MA0159.1 | 0.875329 |
MA0160.1 | 0.600559 |
MA0161.1 | 0 |
MA0162.1 | 0.347838 |
MA0163.1 | 0.813808 |
MA0164.1 | 0.738243 |
MA0080.2 | 1.02158 |
MA0018.2 | 1.69036 |
MA0099.2 | 0.629739 |
MA0079.2 | 0.35176 |
MA0102.2 | 1.58513 |
MA0258.1 | 0.788656 |
MA0259.1 | 0.893594 |
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 |
---|---|---|---|---|
BCL3#602 | 2 | 11.5157009345794 | 0.0116272534680164 | 0.0424787044791744 |
GATA1#2623 | 3 | 6.78015407190022 | 0.00676576398334856 | 0.0287496795775466 |
GATA2#2624 | 3 | 6.372465866777 | 0.00805882130874255 | 0.0318881275541321 |
SP1#6667 | 4 | 3.7989209187606 | 0.0105224661679851 | 0.0389452067516547 |
SREBF1#6720 | 2 | 15.6686164801628 | 0.00641128316580946 | 0.0278902033719583 |
USF2#7392 | 3 | 6.4960986925348 | 0.00763431981530056 | 0.0314562167984446 |
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.