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 601 to 650 of 77072 in total

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description\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
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green\vspace{3pt}}\\
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26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]\vspace{3pt}}}&\multirow{8}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
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1.01532\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
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22.9\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
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1.0173\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
197.228\vspace{3pt}}\\\cline{3-4}\cline{7-9}
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1.02639\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
45129.7\vspace{3pt}}\\\cline{2-3}\cline{6-9}
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2969.8\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
29658.6\vspace{3pt}}\\\cline{3-4}\cline{7-9}
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419.84\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
6278.32\vspace{3pt}}\\\cline{3-3}\cline{6-9}
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1795\vspace{3pt}}&&&\parbox{\wcF}{\vspace{3pt}\noindent
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8126.5\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
262.04\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
8388.54\vspace{3pt}}\\\cline{3-4}\cline{6-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
2033\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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62.382\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.688\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
64.07\vspace{3pt}}\\\cline{3-4}\cline{7-9}
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2324\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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217.112\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.004\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
218.116\vspace{3pt}}\\\cline{3-4}\cline{6-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
2363\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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72.5927\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
2.4527\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
75.0454\vspace{3pt}}\\\cline{3-4}\cline{7-9}
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2828\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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200.64\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
3.412\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
197.228\vspace{3pt}}\\\cline{3-4}\cline{7-9}
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4046\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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46320.5\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1190.8\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
45129.7\vspace{3pt}}\\\cline{1-4}\cline{6-9}
\multirow{10}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [source:swissprot;acc:q13200]\vspace{3pt}}}&\multirow{8}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
Divided\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
1241\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Measured\vspace{3pt}}&&\multirow{3}{*}{\parbox{\wcF}{\vspace{3pt}\noindent
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6436.19\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.08451\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
6980.13\vspace{3pt}}\\\cline{3-4}\cline{7-9}
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1395\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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65.478\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.03987\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
68.0886\vspace{3pt}}\\\cline{3-4}\cline{7-9}
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1538\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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1.11278\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
34111.1\vspace{3pt}}\\\cline{3-4}\cline{6-9}
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1918\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}&&\multirow{2}{*}{\parbox{\wcF}{\vspace{3pt}\noindent
Low confidence\vspace{3pt}}}&\parbox{\wcG}{\vspace{3pt}\noindent
199.382\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.01972\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
195.527\vspace{3pt}}\\\cline{3-4}\cline{7-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
2168\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Measured\vspace{3pt}}&&&\parbox{\wcG}{\vspace{3pt}\noindent
8260.81\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.03153\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
8521.25\vspace{3pt}}\\\cline{3-4}\cline{6-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
2175\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}&&\parbox{\wcF}{\vspace{3pt}\noindent
High confidence\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
210.209\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.00671\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
208.808\vspace{3pt}}\\\cline{3-4}\cline{6-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
2354\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}&&\multirow{2}{*}{\parbox{\wcF}{\vspace{3pt}\noindent
Low confidence\vspace{3pt}}}&\parbox{\wcG}{\vspace{3pt}\noindent
73.2904\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.03403\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
75.7848\vspace{3pt}}\\\cline{3-4}\cline{7-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
4368\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Squared\vspace{3pt}}&&&\parbox{\wcG}{\vspace{3pt}\noindent
47022.7\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.02339\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
45948.2\vspace{3pt}}\\\cline{2-4}\cline{6-9}
&\multirow{2}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
Subtracted\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
986\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Measured\vspace{3pt}}&&\multirow{2}{*}{\parbox{\wcF}{\vspace{3pt}\noindent
High confidence\vspace{3pt}}}&\parbox{\wcG}{\vspace{3pt}\noindent
6436.19\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
543.94\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
6980.13\vspace{3pt}}\\\cline{3-4}\cline{7-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
1014\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Squared\vspace{3pt}}&&&\parbox{\wcG}{\vspace{3pt}\noindent
30653.9\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
3457.2\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
34111.1\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/