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 101 to 150 of 77072 in total 
Filtered: 1

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\parbox{\wcA}{\vspace{3pt}\noindent
description\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
Network Comparison Type\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
Rank\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Value Type\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
Interaction Map\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
red\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
network\_comparison\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
green\vspace{3pt}}\\
\hline
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\multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
1-aminocyclopropane-1-carboxylate synthase. [source:refseq;acc:nm\_032592]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
Subtracted\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
1941\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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8065.05\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
257.99\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
8323.04\vspace{3pt}}\\\cline{3-4}\cline{6-8}
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2688\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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72.5914\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
2.3827\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
74.9741\vspace{3pt}}\\\cline{3-4}\cline{6-8}
&&\parbox{\wcC}{\vspace{3pt}\noindent
3432\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}&&\parbox{\wcF}{\vspace{3pt}\noindent
199.702\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
2.995\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
196.707\vspace{3pt}}\\\cline{3-4}\cline{6-8}
&&\parbox{\wcC}{\vspace{3pt}\noindent
3567\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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45400.4\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1375.2\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
44025.2\vspace{3pt}}\\\cline{1-4}\cline{6-8}
\multirow{16}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4 (ec 3.1.4.11) (phosphoinositide phospholipase c) (plc-beta-4) (phospholipase c-beta-4). [source:swissprot;acc:q15147]\vspace{3pt}}}&\multirow{8}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
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2882\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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7948.01\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.02859\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
8175.27\vspace{3pt}}\\\cline{3-4}\cline{6-8}
&&\parbox{\wcC}{\vspace{3pt}\noindent
2991\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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45624.8\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.03575\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
44050.1\vspace{3pt}}\\\cline{3-8}
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3126\vspace{3pt}}}&\parbox{\wcD}{\vspace{3pt}\noindent
Measured\vspace{3pt}}&\multirow{4}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
High confidence\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcF}{\vspace{3pt}\noindent
0.00001\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcG}{\vspace{3pt}\noindent
1\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcH}{\vspace{3pt}\noindent
0.00001\vspace{3pt}}}\\\cline{4-4}
&&&\parbox{\wcD}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}&&&&\\\cline{4-4}
&&&\parbox{\wcD}{\vspace{3pt}\noindent
Squared\vspace{3pt}}&&&&\\\cline{4-4}
&&&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}}&&&&\\\cline{3-3}\cline{5-8}
&&\parbox{\wcC}{\vspace{3pt}\noindent
3189\vspace{3pt}}&&\multirow{4}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
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71.5946\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.03146\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
73.847\vspace{3pt}}\\\cline{3-4}\cline{6-8}
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3585\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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202.517\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.01447\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
199.628\vspace{3pt}}\\\cline{2-4}\cline{6-8}
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2819\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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45624.8\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1574.7\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
44050.1\vspace{3pt}}\\\cline{3-4}\cline{6-8}
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2902\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
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7948.01\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
227.26\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
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0\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcG}{\vspace{3pt}\noindent
0\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcH}{\vspace{3pt}\noindent
0\vspace{3pt}}}\\\cline{4-4}
&&&\parbox{\wcD}{\vspace{3pt}\noindent
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&&&\parbox{\wcD}{\vspace{3pt}\noindent
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3244\vspace{3pt}}&&\multirow{2}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
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71.5946\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
2.2524\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
73.847\vspace{3pt}}\\\cline{3-4}\cline{6-8}
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3567\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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202.517\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
2.889\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
199.628\vspace{3pt}}\\\hline
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10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [source:swissprot;acc:q04984]\vspace{3pt}}}&\multirow{8}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
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588\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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23526.4\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.18502\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
27879.3\vspace{3pt}}\\\cline{3-4}\cline{6-8}
&&\parbox{\wcC}{\vspace{3pt}\noindent
1136\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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5790.65\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.08864\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
6303.92\vspace{3pt}}\\\cline{3-4}\cline{6-8}
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1907\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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63.4353\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.02906\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
65.2789\vspace{3pt}}\\\cline{3-4}\cline{6-8}
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1963\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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211.633\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.00978\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
213.703\vspace{3pt}}\\\cline{3-8}
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2182\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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8130.62\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.03148\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
8386.58\vspace{3pt}}\\\cline{3-4}\cline{6-8}
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1.0177\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
196.574\vspace{3pt}}\\\cline{3-4}\cline{6-8}
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3878\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
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46195.2\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.02953\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
44870.2\vspace{3pt}}\\\cline{2-3}\cline{5-8}
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23526.4\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
4352.9\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
27879.3\vspace{3pt}}\\\cline{3-4}\cline{6-8}
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1140\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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5790.65\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
513.27\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
6303.92\vspace{3pt}}\\\cline{3-4}\cline{6-8}
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1902\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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63.4353\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.8436\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
65.2789\vspace{3pt}}\\\cline{3-4}\cline{6-8}
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1933\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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211.633\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
2.07\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
213.703\vspace{3pt}}\\\cline{3-8}
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2020\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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8130.62\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
255.96\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
8386.58\vspace{3pt}}\\\cline{3-4}\cline{6-8}
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72.718\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
2.4494\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
75.1674\vspace{3pt}}\\\cline{3-4}\cline{6-8}
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2668\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}&&\parbox{\wcF}{\vspace{3pt}\noindent
200.053\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
3.479\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
196.574\vspace{3pt}}\\\cline{3-4}\cline{6-8}
&&\parbox{\wcC}{\vspace{3pt}\noindent
3743\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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46195.2\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1325\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
44870.2\vspace{3pt}}\\\cline{1-4}\cline{6-8}
\multirow{14}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [source:swissprot;acc:o75891]\vspace{3pt}}}&\multirow{8}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
Divided\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
1632\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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71.5773\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.03601\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
74.1551\vspace{3pt}}\\\cline{3-4}\cline{6-8}
&&\parbox{\wcC}{\vspace{3pt}\noindent
1693\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Measured\vspace{3pt}}&&\parbox{\wcF}{\vspace{3pt}\noindent
7981.12\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.03323\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
8246.34\vspace{3pt}}\\\cline{3-4}\cline{6-8}
&&\parbox{\wcC}{\vspace{3pt}\noindent
1873\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}&&\parbox{\wcF}{\vspace{3pt}\noindent
203.414\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.01985\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
199.455\vspace{3pt}}\\\cline{3-8}
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2922\vspace{3pt}}}&\parbox{\wcD}{\vspace{3pt}\noindent
Measured\vspace{3pt}}&\multirow{4}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
High confidence\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcF}{\vspace{3pt}\noindent
0.00001\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcG}{\vspace{3pt}\noindent
1\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcH}{\vspace{3pt}\noindent
0.00001\vspace{3pt}}}\\\cline{4-4}
&&&\parbox{\wcD}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}&&&&\\\cline{4-4}
&&&\parbox{\wcD}{\vspace{3pt}\noindent
Squared\vspace{3pt}}&&&&\\\cline{4-4}
&&&\parbox{\wcD}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}&&&&\\\cline{3-8}
&&\parbox{\wcC}{\vspace{3pt}\noindent
4003\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Squared\vspace{3pt}}&\multirow{4}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
Low confidence\vspace{3pt}}}&\parbox{\wcF}{\vspace{3pt}\noindent
45711.3\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.02811\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
44461.5\vspace{3pt}}\\\cline{2-4}\cline{6-8}
&\multirow{6}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
Subtracted\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
1700\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Measured\vspace{3pt}}&&\parbox{\wcF}{\vspace{3pt}\noindent
7981.12\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
265.22\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
8246.34\vspace{3pt}}\\\cline{3-4}\cline{6-8}
&&\parbox{\wcC}{\vspace{3pt}\noindent
1730\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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71.5773\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
2.5778\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
74.1551\vspace{3pt}}\\\cline{3-4}\cline{6-8}
&&\parbox{\wcC}{\vspace{3pt}\noindent
1795\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}&&\parbox{\wcF}{\vspace{3pt}\noindent
203.414\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
3.959\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
199.455\vspace{3pt}}\\\cline{3-8}
&&\multirow{3}{*}{\parbox{\wcC}{\vspace{3pt}\noindent
2922\vspace{3pt}}}&\parbox{\wcD}{\vspace{3pt}\noindent
Measured\vspace{3pt}}&\multirow{3}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
High confidence\vspace{3pt}}}&\multirow{3}{*}{\parbox{\wcF}{\vspace{3pt}\noindent
0\vspace{3pt}}}&\multirow{3}{*}{\parbox{\wcG}{\vspace{3pt}\noindent
0\vspace{3pt}}}&\multirow{3}{*}{\parbox{\wcH}{\vspace{3pt}\noindent
0\vspace{3pt}}}\\\cline{4-4}
&&&\parbox{\wcD}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}&&&&\\\cline{4-4}
&&&\parbox{\wcD}{\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/