Coexpression cluster:C1047: Difference between revisions
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{{Coexpression_clusters | 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regulation of transcription, DNA-dependent!0.002668471739994!5606;2309$GO:0045941!positive regulation of transcription!0.002668471739994!5606;2309$GO:0045935!positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.002668471739994!5606;2309$GO:0031325!positive regulation of cellular metabolic process!0.00293335680241988!5606;2309$GO:0009893!positive regulation of metabolic process!0.00293335680241988!5606;2309$GO:0045648!positive regulation of erythrocyte differentiation!0.00544534052623127!2309$GO:0045646!regulation of erythrocyte differentiation!0.0079495422567252!2309$GO:0004708!MAP kinase kinase activity!0.0079495422567252!5606$GO:0004712!protein serine/threonine/tyrosine kinase activity!0.0079495422567252!5606$GO:0045639!positive regulation of myeloid cell differentiation!0.0079495422567252!2309$GO:0048522!positive regulation of cellular process!0.0079495422567252!5606;2309$GO:0048518!positive regulation of biological process!0.00903133988169789!5606;2309$GO:0030218!erythrocyte differentiation!0.0158625041483939!2309$GO:0045637!regulation of myeloid cell differentiation!0.0158625041483939!2309$GO:0045597!positive regulation of cell differentiation!0.0204618228353415!2309$GO:0051094!positive regulation of developmental process!0.027745483969377!2309$GO:0030099!myeloid cell differentiation!0.0295656607028872!2309$GO:0019901!protein kinase binding!0.0300962908074367!2309$GO:0019900!kinase binding!0.0340005992307244!2309$GO:0045944!positive regulation of transcription from RNA polymerase II promoter!0.0393274420359954!2309$GO:0045860!positive regulation of protein kinase activity!0.0393274420359954!5606$GO:0045595!regulation of cell differentiation!0.0393274420359954!2309$GO:0033674!positive regulation of kinase activity!0.0393274420359954!5606$GO:0051347!positive regulation of transferase activity!0.0393274420359954!5606$GO:0030097!hemopoiesis!0.0393274420359954!2309$GO:0006355!regulation of transcription, DNA-dependent!0.0393274420359954!5606;2309$GO:0048534!hemopoietic or lymphoid organ development!0.0393274420359954!2309$GO:0006351!transcription, DNA-dependent!0.0393274420359954!5606;2309$GO:0032774!RNA biosynthetic process!0.0393274420359954!5606;2309$GO:0002520!immune system development!0.0395387988639219!2309$GO:0045449!regulation of transcription!0.0396816272126048!5606;2309$GO:0019219!regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0396816272126048!5606;2309$GO:0006350!transcription!0.0396816272126048!5606;2309$GO:0010468!regulation of gene expression!0.0396816272126048!5606;2309$GO:0031323!regulation of cellular metabolic process!0.0396816272126048!5606;2309$GO:0050793!regulation of developmental process!0.0396816272126048!2309$GO:0045859!regulation of protein kinase activity!0.0396816272126048!5606$GO:0043549!regulation of kinase activity!0.0396816272126048!5606$GO:0051338!regulation of transferase activity!0.0396816272126048!5606$GO:0019222!regulation of metabolic process!0.0396816272126048!5606;2309$GO:0016070!RNA metabolic process!0.0396816272126048!5606;2309$GO:0043085!positive regulation of catalytic activity!0.0396816272126048!5606$GO:0019899!enzyme binding!0.0446688293427135!2309$GO:0004713!protein-tyrosine kinase activity!0.0446688293427135!5606$GO:0016563!transcription activator activity!0.0446688293427135!2309|id=C1047|ontology_enrichment_celltype=CL:0000473!2.81e-27!48;CL:0000234!2.81e-27!48;CL:0000860!2.06e-26!42;CL:0002057!2.06e-26!42;CL:0000766!3.39e-25!72;CL:0000839!1.81e-21!66;CL:0000557!3.37e-21!67;CL:0002009!7.95e-20!61;CL:0002194!7.74e-19!59;CL:0000576!7.74e-19!59;CL:0000040!7.74e-19!59;CL:0000559!7.74e-19!59;CL:0000325!7.21e-18!87;CL:0000763!1.40e-08!108;CL:0000049!1.40e-08!108|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002390!2.45e-21!98;UBERON:0003061!2.45e-21!98;UBERON:0002193!7.53e-20!108;UBERON:0002371!1.67e-19!76;UBERON:0001474!1.74e-17!82;UBERON:0003081!2.78e-17!203;UBERON:0002204!6.35e-16!167;UBERON:0001434!7.40e-16!100;UBERON:0002405!1.60e-15!93;UBERON:0000468!3.65e-15!656;UBERON:0004765!6.39e-15!90;UBERON:0000926!3.66e-14!315;UBERON:0004120!3.66e-14!315;UBERON:0006603!3.66e-14!315;UBERON:0000467!4.78e-14!624;UBERON:0000480!5.77e-14!625;UBERON:0000923!4.83e-10!560;UBERON:0010316!4.83e-10!560;UBERON:0005291!4.83e-10!560;UBERON:0006598!4.83e-10!560;UBERON:0010317!4.83e-10!560;UBERON:0002532!4.83e-10!560;UBERON:0002050!1.03e-09!564;UBERON:0005423!1.19e-09!581;UBERON:0000922!1.69e-09!592;UBERON:0007023!5.63e-07!114|pathway_enrichment=2.92938943019595e-05;0.0101306962986864;2;155;TGF-beta Receptor Signaling Pathway (Wikipathways):WP366!3.20085191111734e-05;0.0101306962986864;2;162;Insulin Signaling 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Latest revision as of 11:36, 17 September 2013
Full id: C1047_Whole_blood_CD14_Neutrophils_Eosinophils_Reticulocytes_Mast
Phase1 CAGE Peaks
| Hg19::chr17:21188012..21188031,+ | p1@MAP2K3 |
| Hg19::chr17:21188043..21188069,+ | p2@MAP2K3 |
| Hg19::chr17:21188075..21188079,+ | p4@MAP2K3 |
| Hg19::chr4:2801321..2801334,+ | p@chr4:2801321..2801334 + |
| Hg19::chr6:108882109..108882173,+ | p2@FOXO3 |
| Hg19::chr6:108882364..108882391,+ | p4@FOXO3 |
| Hg19::chr7:35469..35507,- | p1@ENST00000469418 |
| Hg19::chrX:67718803..67718831,- | p@chrX:67718803..67718831 - |
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
| p.value | FDR | nGenes | nPathway | Name |
|---|---|---|---|---|
| 2.92938943019595e-05 | 0.0101306962986864 | 2 | 155 | TGF-beta Receptor Signaling Pathway (Wikipathways):WP366 |
| 3.20085191111734e-05 | 0.0101306962986864 | 2 | 162 | Insulin Signaling (Wikipathways):WP481 |
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:0045893 | positive regulation of transcription, DNA-dependent | 0.002668471739994 |
| GO:0045941 | positive regulation of transcription | 0.002668471739994 |
| GO:0045935 | positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.002668471739994 |
| GO:0031325 | positive regulation of cellular metabolic process | 0.00293335680241988 |
| GO:0009893 | positive regulation of metabolic process | 0.00293335680241988 |
| GO:0045648 | positive regulation of erythrocyte differentiation | 0.00544534052623127 |
| GO:0045646 | regulation of erythrocyte differentiation | 0.0079495422567252 |
| GO:0004708 | MAP kinase kinase activity | 0.0079495422567252 |
| GO:0004712 | protein serine/threonine/tyrosine kinase activity | 0.0079495422567252 |
| GO:0045639 | positive regulation of myeloid cell differentiation | 0.0079495422567252 |
| GO:0048522 | positive regulation of cellular process | 0.0079495422567252 |
| GO:0048518 | positive regulation of biological process | 0.00903133988169789 |
| GO:0030218 | erythrocyte differentiation | 0.0158625041483939 |
| GO:0045637 | regulation of myeloid cell differentiation | 0.0158625041483939 |
| GO:0045597 | positive regulation of cell differentiation | 0.0204618228353415 |
| GO:0051094 | positive regulation of developmental process | 0.027745483969377 |
| GO:0030099 | myeloid cell differentiation | 0.0295656607028872 |
| GO:0019901 | protein kinase binding | 0.0300962908074367 |
| GO:0019900 | kinase binding | 0.0340005992307244 |
| GO:0045944 | positive regulation of transcription from RNA polymerase II promoter | 0.0393274420359954 |
| GO:0045860 | positive regulation of protein kinase activity | 0.0393274420359954 |
| GO:0045595 | regulation of cell differentiation | 0.0393274420359954 |
| GO:0033674 | positive regulation of kinase activity | 0.0393274420359954 |
| GO:0051347 | positive regulation of transferase activity | 0.0393274420359954 |
| GO:0030097 | hemopoiesis | 0.0393274420359954 |
| GO:0006355 | regulation of transcription, DNA-dependent | 0.0393274420359954 |
| GO:0048534 | hemopoietic or lymphoid organ development | 0.0393274420359954 |
| GO:0006351 | transcription, DNA-dependent | 0.0393274420359954 |
| GO:0032774 | RNA biosynthetic process | 0.0393274420359954 |
| GO:0002520 | immune system development | 0.0395387988639219 |
| GO:0045449 | regulation of transcription | 0.0396816272126048 |
| GO:0019219 | regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0396816272126048 |
| GO:0006350 | transcription | 0.0396816272126048 |
| GO:0010468 | regulation of gene expression | 0.0396816272126048 |
| GO:0031323 | regulation of cellular metabolic process | 0.0396816272126048 |
| GO:0050793 | regulation of developmental process | 0.0396816272126048 |
| GO:0045859 | regulation of protein kinase activity | 0.0396816272126048 |
| GO:0043549 | regulation of kinase activity | 0.0396816272126048 |
| GO:0051338 | regulation of transferase activity | 0.0396816272126048 |
| GO:0019222 | regulation of metabolic process | 0.0396816272126048 |
| GO:0016070 | RNA metabolic process | 0.0396816272126048 |
| GO:0043085 | positive regulation of catalytic activity | 0.0396816272126048 |
| GO:0019899 | enzyme binding | 0.0446688293427135 |
| GO:0004713 | protein-tyrosine kinase activity | 0.0446688293427135 |
| GO:0016563 | transcription activator activity | 0.0446688293427135 |
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 |
|---|---|---|
| defensive cell | 2.81e-27 | 48 |
| phagocyte | 2.81e-27 | 48 |
| classical monocyte | 2.06e-26 | 42 |
| CD14-positive, CD16-negative classical monocyte | 2.06e-26 | 42 |
| myeloid leukocyte | 3.39e-25 | 72 |
| myeloid lineage restricted progenitor cell | 1.81e-21 | 66 |
| granulocyte monocyte progenitor cell | 3.37e-21 | 67 |
| macrophage dendritic cell progenitor | 7.95e-20 | 61 |
| monopoietic cell | 7.74e-19 | 59 |
| monocyte | 7.74e-19 | 59 |
| monoblast | 7.74e-19 | 59 |
| promonocyte | 7.74e-19 | 59 |
| stuff accumulating cell | 7.21e-18 | 87 |
| myeloid cell | 1.40e-08 | 108 |
| common myeloid progenitor | 1.40e-08 | 108 |
| Ontology term | p-value | n |
|---|---|---|
| hematopoietic system | 2.45e-21 | 98 |
| blood island | 2.45e-21 | 98 |
| hemolymphoid system | 7.53e-20 | 108 |
| bone marrow | 1.67e-19 | 76 |
| bone element | 1.74e-17 | 82 |
| lateral plate mesoderm | 2.78e-17 | 203 |
| musculoskeletal system | 6.35e-16 | 167 |
| skeletal system | 7.40e-16 | 100 |
| immune system | 1.60e-15 | 93 |
| multi-cellular organism | 3.65e-15 | 656 |
| skeletal element | 6.39e-15 | 90 |
| mesoderm | 3.66e-14 | 315 |
| mesoderm-derived structure | 3.66e-14 | 315 |
| presumptive mesoderm | 3.66e-14 | 315 |
| anatomical system | 4.78e-14 | 624 |
| anatomical group | 5.77e-14 | 625 |
| germ layer | 4.83e-10 | 560 |
| germ layer / neural crest | 4.83e-10 | 560 |
| embryonic tissue | 4.83e-10 | 560 |
| presumptive structure | 4.83e-10 | 560 |
| germ layer / neural crest derived structure | 4.83e-10 | 560 |
| epiblast (generic) | 4.83e-10 | 560 |
| embryonic structure | 1.03e-09 | 564 |
| developing anatomical structure | 1.19e-09 | 581 |
| embryo | 1.69e-09 | 592 |
| adult organism | 5.63e-07 | 114 |
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 | 0.797136 |
| MA0004.1 | 0.455723 |
| MA0006.1 | 0.812175 |
| MA0007.1 | 0.437331 |
| MA0009.1 | 0.918715 |
| MA0014.1 | 1.03236 |
| MA0017.1 | 0.337901 |
| MA0019.1 | 0.602411 |
| MA0024.1 | 0.813542 |
| MA0025.1 | 1.05265 |
| MA0027.1 | 2.5321 |
| MA0028.1 | 0.315574 |
| MA0029.1 | 0.832916 |
| MA0030.1 | 0.821423 |
| MA0031.1 | 0.756713 |
| MA0038.1 | 0.557409 |
| MA0040.1 | 0.838784 |
| MA0041.1 | 0.474018 |
| MA0042.1 | 0.442535 |
| MA0043.1 | 0.919032 |
| MA0046.1 | 0.90778 |
| MA0048.1 | 0.653157 |
| MA0050.1 | 0.443405 |
| MA0051.1 | 0.553205 |
| MA0052.1 | 0.842664 |
| MA0055.1 | 6.62303 |
| MA0056.1 | 0 |
| MA0057.1 | 0.305162 |
| MA0058.1 | 0.362328 |
| MA0059.1 | 0.361075 |
| MA0060.1 | 1.06021 |
| MA0061.1 | 0.961853 |
| MA0063.1 | 0 |
| MA0066.1 | 0.557833 |
| MA0067.1 | 1.23721 |
| MA0068.1 | 0.415214 |
| MA0069.1 | 0.903908 |
| MA0070.1 | 0.892666 |
| MA0071.1 | 0.518907 |
| MA0072.1 | 0.888148 |
| MA0073.1 | 0.131075 |
| MA0074.1 | 0.552456 |
| MA0076.1 | 0.377799 |
| MA0077.1 | 0.880402 |
| MA0078.1 | 0.652193 |
| MA0081.1 | 0.361233 |
| MA0083.1 | 0.926258 |
| MA0084.1 | 1.42483 |
| MA0087.1 | 0.885691 |
| MA0088.1 | 0.770971 |
| MA0089.1 | 0 |
| MA0090.1 | 0.391903 |
| MA0091.1 | 0.458301 |
| MA0092.1 | 0.421159 |
| MA0093.1 | 0.818737 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.571227 |
| MA0101.1 | 0.30624 |
| MA0103.1 | 0.291333 |
| MA0105.1 | 2.64083 |
| MA0106.1 | 1.45807 |
| MA0107.1 | 0.236528 |
| MA0108.2 | 0.753643 |
| MA0109.1 | 0 |
| MA0111.1 | 0.405141 |
| MA0113.1 | 0.614917 |
| MA0114.1 | 0.231781 |
| MA0115.1 | 1.1606 |
| MA0116.1 | 0.239768 |
| MA0117.1 | 0.956472 |
| MA0119.1 | 0.345493 |
| MA0122.1 | 0.982472 |
| MA0124.1 | 1.11898 |
| MA0125.1 | 1.0347 |
| MA0130.1 | 0 |
| MA0131.1 | 0.670358 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.949204 |
| MA0136.1 | 0.564434 |
| MA0139.1 | 0.155155 |
| MA0140.1 | 1.28413 |
| MA0141.1 | 0.359385 |
| MA0142.1 | 0.724856 |
| MA0143.1 | 0.615094 |
| MA0144.1 | 0.218541 |
| MA0145.1 | 2.31266 |
| MA0146.1 | 3.51017 |
| MA0147.1 | 0.243042 |
| MA0148.1 | 0.480298 |
| MA0149.1 | 0.506665 |
| MA0062.2 | 0.485915 |
| MA0035.2 | 0.515566 |
| MA0039.2 | 4.44385 |
| MA0138.2 | 0.653421 |
| MA0002.2 | 0.531206 |
| MA0137.2 | 0.321796 |
| MA0104.2 | 0.189646 |
| MA0047.2 | 0.586412 |
| MA0112.2 | 0.458158 |
| MA0065.2 | 0.490252 |
| MA0150.1 | 0.386144 |
| MA0151.1 | 0 |
| MA0152.1 | 0.52279 |
| MA0153.1 | 1.01778 |
| MA0154.1 | 0.274121 |
| MA0155.1 | 1.64163 |
| MA0156.1 | 0.865715 |
| MA0157.1 | 0.697424 |
| MA0158.1 | 0 |
| MA0159.1 | 0.682702 |
| MA0160.1 | 0.495355 |
| MA0161.1 | 0 |
| MA0162.1 | 4.37832 |
| MA0163.1 | 0.75401 |
| MA0164.1 | 0.627336 |
| MA0080.2 | 0.818924 |
| MA0018.2 | 0.599912 |
| MA0099.2 | 1.29876 |
| MA0079.2 | 7.67909 |
| MA0102.2 | 1.46209 |
| MA0258.1 | 0.603127 |
| MA0259.1 | 1.29349 |
| 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 |
|---|---|---|---|---|
| CHD2#1106 | 5 | 6.46501427132304 | 0.000367624325807319 | 0.00366078537023175 |
| FOSL2#2355 | 3 | 6.34882522671063 | 0.00921194665864107 | 0.0348266605278485 |
| HEY1#23462 | 6 | 3.03008328232928 | 0.00400172346648327 | 0.0191854570839169 |
| MAFK#7975 | 3 | 10.1627749266862 | 0.00244557310713952 | 0.0137681639661767 |
| NFYA#4800 | 3 | 6.90959276243645 | 0.00727972723713068 | 0.030122323015796 |
| NFYB#4801 | 3 | 6.28492247007617 | 0.00947376901248262 | 0.0356963331371193 |
| PBX3#5090 | 3 | 8.21794225752905 | 0.00447320658280844 | 0.0211670165512179 |
| REST#5978 | 4 | 4.82501435806401 | 0.00572073539826954 | 0.0257873833251272 |
| SIN3A#25942 | 5 | 3.38055295425946 | 0.00734222696117028 | 0.0303652968596865 |
| SP2#6668 | 3 | 9.80757393519174 | 0.00270718466508561 | 0.0148863085998461 |
| TAF1#6872 | 6 | 2.50728471430897 | 0.0111173447561386 | 0.0408832524290973 |
| TBP#6908 | 6 | 2.78007801532229 | 0.00639018112126301 | 0.0278030380821358 |
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.
