Scientific

MK5 Microarray Data


Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Hugo measured Gene Rank description expected final
Results: HTML CSV LaTeX Showing element 51 to 100 of 3206 in total
Hugo: 
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0.266704148\vspace{3pt}}\\\cline{1-2}\cline{4-5} \parbox{\wcA}{\vspace{3pt}\noindent 0.0436957\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 2522\vspace{3pt}}&&\parbox{\wcD}{\vspace{3pt}\noindent 0.203458\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.21476521\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0444453\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 3004\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent ENDO-BETA-N-ACETYLGLUCOSAMINIDASE. \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.352603\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.126049126\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.044904\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 1700\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.188793\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.237847802\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0454701\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 2677\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE (EC 2.7.7.12) (GAL-1-P URIDYLYLTRANSFERASE) (UDP-GLUCOSE--HEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE). \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.217847\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.208724931\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0483186\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 356\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.171674\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.281455549\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.048624\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 3090\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent METHYLTRANSFERASE LIKE 2. \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.498014\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.097635809\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0486609\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 2769\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent SIMILAR TO ZINC FINGER PROTEIN 277. \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.241353\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.201617133\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0488461\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 1642\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.204356\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.239024545\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.050323\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 1646\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent MYOSIN VI. \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.210535\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.23902439\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0503334\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 308\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent MITOCHONDRIAL 28S RIBOSOMAL PROTEIN S32 (S32MT) (MRP-S32) (PTD007) (HSPC204). \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.170278\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.295595438\vspace{3pt}}\\\hline nd{longtable}
Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots

- http://analysis.yellowcouch.org/