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 Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.
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description Gene Network Comparison Type Rank Value Type Filtered Interaction Map red network_comparison green
Results: HTML CSV LaTeX
Showing element 76474 to 76523 of 77072 in total

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8281.29\vspace{3pt}}\\\cline{1-4}\cline{7-9}
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1812\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Measured\vspace{3pt}}&&&\parbox{\wcG}{\vspace{3pt}\noindent
4392.63\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
383.56\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
4776.19\vspace{3pt}}\\\cline{3-4}\cline{6-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
1897\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}}&&\parbox{\wcF}{\vspace{3pt}\noindent
Low confidence\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
71.9383\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
2.5457\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
74.484\vspace{3pt}}\\\cline{3-3}\cline{6-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
1927\vspace{3pt}}&&&\multirow{2}{*}{\parbox{\wcF}{\vspace{3pt}\noindent
High confidence\vspace{3pt}}}&\parbox{\wcG}{\vspace{3pt}\noindent
54.1965\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.8266\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
56.0231\vspace{3pt}}\\\cline{3-4}\cline{7-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
2433\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}&&&\parbox{\wcG}{\vspace{3pt}\noindent
235.812\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
0.724\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
235.088\vspace{3pt}}\\\cline{3-4}\cline{6-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
3438\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
Measured\vspace{3pt}}}&&\multirow{4}{*}{\parbox{\wcF}{\vspace{3pt}\noindent
Low confidence\vspace{3pt}}}&\parbox{\wcG}{\vspace{3pt}\noindent
8083.75\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
208.8\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
8292.55\vspace{3pt}}\\\cline{1-3}\cline{5-5}\cline{7-9}
\multirow{3}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
zinc finger protein loc163140 (fragment). [source:sptrembl;acc:q86wm6]\vspace{3pt}}}&\multirow{3}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
Divided\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
198\vspace{3pt}}&&\multirow{3}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
0\vspace{3pt}}}&&\parbox{\wcG}{\vspace{3pt}\noindent
2350.92\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.19455\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
1968.04\vspace{3pt}}\\\cline{3-4}\cline{7-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
242\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}&&&\parbox{\wcG}{\vspace{3pt}\noindent
45.298\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.11284\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
40.7049\vspace{3pt}}\\\cline{3-4}\cline{7-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
254\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}&&&\parbox{\wcG}{\vspace{3pt}\noindent
4257.81\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.14021\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
4854.79\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/