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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

  • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1230 to 1279 of 1892 in total
    Network Comparison Type: Subtracted
    Interaction Map: High confidence
    Filtered: 1
    red: 0
    green: 0
    network\_comparison: 0
    \def\wcA{0.25\textwidth} \def\wcB{0.25\textwidth} \def\wcC{0.25\textwidth} \begin{longtable}{|c|c|c|} \hline \parbox{\wcA}{\vspace{3pt}\noindent Rank\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent description\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent Value Type\vspace{3pt}}\\ \hline \hline \multirow{3}{*}{\parbox{\wcA}{\vspace{3pt}\noindent 3063\vspace{3pt}}}&\multirow{3}{*}{\parbox{\wcB}{\vspace{3pt}\noindent mitochondrial 28s ribosomal protein s30 (s30mt) (mrp-s30) (programmed cell death protein 9) (bm047). [source:swissprot;acc:q9np92]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent Ranked\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Squared\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Rooted\vspace{3pt}}\\\hline \multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent 3064\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent complement component c7 precursor. [source:swissprot;acc:p10643]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent Measured\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Ranked\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Squared\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Rooted\vspace{3pt}}\\\hline \multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent 3065\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent wnt1 inducible signaling pathway protein 3 isoform 1; wnt-1 signaling pathway protein 3; wnt1 signaling pathway protein 3; wnt-1 inducible signaling pathway protein 3. [source:refseq;acc:nm\_003880]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent Measured\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Ranked\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Squared\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Rooted\vspace{3pt}}\\\hline \multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent 3066\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent vascular endothelial growth factor a precursor (vegf-a) (vascular permeability factor) (vpf). [source:swissprot;acc:p15692]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent Measured\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Ranked\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Squared\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Rooted\vspace{3pt}}\\\hline \multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent 3067\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent retinoic acid receptor rxr-beta. [source:swissprot;acc:p28702]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent Measured\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Ranked\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Squared\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Rooted\vspace{3pt}}\\\hline \multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent 3068\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent headcase homolog; hhdc for homolog of drosophila headcase. [source:refseq;acc:nm\_016217]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent Measured\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Ranked\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Squared\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Rooted\vspace{3pt}}\\\hline \multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent 3069\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent bone morphogenetic protein 5 precursor (bmp-5). [source:swissprot;acc:p22003]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent Measured\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Ranked\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Squared\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Rooted\vspace{3pt}}\\\hline \multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent 3070\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent mam domain containing glycosylphosphatidylinositol anchor 1; glycosyl-phosphatidyl-inositol-mam. [source:refseq;acc:nm\_153487]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent Measured\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Ranked\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Squared\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Rooted\vspace{3pt}}\\\hline \multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent 3071\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent serine/threonine kinase 38; serine threonine protein kinase. [source:refseq;acc:nm\_007271]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent Measured\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Ranked\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Squared\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Rooted\vspace{3pt}}\\\hline \multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent 3072\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent pak1 interacting protein 1; pak1-interacting protein; pak/plc-interacting protein 1. [source:refseq;acc:nm\_017906]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent Measured\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Ranked\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Squared\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Rooted\vspace{3pt}}\\\hline \multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent 3073\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent rwd domain containing 1; ptd013 protein; cgi-24 protein. [source:refseq;acc:nm\_015952]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent Measured\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Ranked\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Squared\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Rooted\vspace{3pt}}\\\hline \multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent 3074\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent tu12b1-ty protein. [source:refseq;acc:nm\_016575]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent Measured\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Ranked\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Squared\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Rooted\vspace{3pt}}\\\hline \multirow{3}{*}{\parbox{\wcA}{\vspace{3pt}\noindent 3075\vspace{3pt}}}&\multirow{3}{*}{\parbox{\wcB}{\vspace{3pt}\noindent ubiquitin carboxyl-terminal hydrolase 5 (ec 3.1.2.15) (ubiquitin thiolesterase 5) (ubiquitin-specific processing protease 5) (deubiquitinating enzyme 5) (isopeptidase t). [source:swissprot;acc:p45974]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent Measured\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Ranked\vspace{3pt}}\\\cline{3-3} &&\parbox{\wcC}{\vspace{3pt}\noindent Squared\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
    - Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
    - Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
    - Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
    - Filtered specifies whether we only included the high confidence microarry measurements or not.

    - http://analysis.yellowcouch.org/