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 1 to 50 of 77072 in total

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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
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Interaction Map\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
red\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
network\_comparison\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
green\vspace{3pt}}\\
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1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]\vspace{3pt}}}&\multirow{16}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
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245.247\vspace{3pt}}\\\cline{3-5}\cline{7-9}
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934.348\vspace{3pt}}\\\cline{4-4}\cline{7-9}
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1.5213\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
18.0183\vspace{3pt}}\\\cline{3-5}\cline{7-9}
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1.6231\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
2765.82\vspace{3pt}}\\\cline{3-4}\cline{7-9}
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63.8686\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.35128\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
47.2654\vspace{3pt}}\\\cline{3-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
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645.504\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.31954\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
851.77\vspace{3pt}}\\\cline{3-4}\cline{7-9}
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1268.51\vspace{3pt}}\\\cline{3-4}\cline{6-9}
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15260.6\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.09822\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
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1.31131\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
6768.05\vspace{3pt}}\\\cline{3-9}
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537\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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16.298\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.04801\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
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13205.3\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.02915\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
13590.3\vspace{3pt}}\\\cline{3-5}\cline{7-9}
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1119\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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1.04654\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
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1.01062\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
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7853.62\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.00597\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
7900.54\vspace{3pt}}\\\cline{4-4}\cline{7-9}
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71.9496\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.00944\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
72.6287\vspace{3pt}}\\\cline{2-9}
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599.947\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
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185.678\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
59.569\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
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67\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
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63.8686\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
16.6032\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
47.2654\vspace{3pt}}\\\cline{3-3}\cline{5-5}\cline{7-9}
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69\vspace{3pt}}&&\multirow{2}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
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11.844\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
6.1743\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
18.0183\vspace{3pt}}\\\cline{3-4}\cline{7-9}
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1723.37\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
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1364.8\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
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645.504\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
206.266\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
851.77\vspace{3pt}}\\\cline{3-4}\cline{7-9}
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319\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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492.79\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
1268.51\vspace{3pt}}\\\cline{3-4}\cline{7-9}
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13205.3\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
385\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
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16.298\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
0.7824\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
17.0804\vspace{3pt}}\\\cline{3-5}\cline{7-9}
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1423\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
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1940\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
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2106.96\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
6768.05\vspace{3pt}}\\\cline{3-4}\cline{6-9}
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199.383\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
2.117\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
201.5\vspace{3pt}}\\\cline{3-4}\cline{7-9}
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7853.62\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
46.92\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
7900.54\vspace{3pt}}\\\cline{3-4}\cline{7-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
4919\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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71.9496\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
0.6791\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
72.6287\vspace{3pt}}\\\cline{1-4}\cline{6-9}
\multirow{16}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [source:swissprot;acc:q99943]\vspace{3pt}}}&\multirow{8}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
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295\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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30807.7\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.27733\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
39351.7\vspace{3pt}}\\\cline{3-4}\cline{7-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
509\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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7551.8\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.14278\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
8630.06\vspace{3pt}}\\\cline{3-4}\cline{7-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
805\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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74.3557\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.0645\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
79.1513\vspace{3pt}}\\\cline{3-4}\cline{6-9}
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885\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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8255.95\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.03993\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
8585.64\vspace{3pt}}\\\cline{3-4}\cline{6-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
1038\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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186.741\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.03148\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
181.041\vspace{3pt}}\\\cline{3-4}\cline{6-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
1092\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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73.5001\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.0386\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
76.3375\vspace{3pt}}\\\cline{3-4}\cline{7-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
1328\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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198.342\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.02218\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
194.038\vspace{3pt}}\\\cline{3-4}\cline{7-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
4562\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
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46617.7\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.01928\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
45736\vspace{3pt}}\\\cline{2-3}\cline{6-9}
&\multirow{8}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
Subtracted\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
274\vspace{3pt}}&&&\multirow{3}{*}{\parbox{\wcF}{\vspace{3pt}\noindent
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30807.7\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
8544\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
39351.7\vspace{3pt}}\\\cline{3-4}\cline{7-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
310\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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7551.8\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1078.26\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
8630.06\vspace{3pt}}\\\cline{3-4}\cline{7-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
610\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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74.3557\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
4.7956\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
79.1513\vspace{3pt}}\\\cline{3-4}\cline{6-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
780\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Measured\vspace{3pt}}&&\multirow{2}{*}{\parbox{\wcF}{\vspace{3pt}\noindent
Low confidence\vspace{3pt}}}&\parbox{\wcG}{\vspace{3pt}\noindent
8255.95\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
329.69\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
8585.64\vspace{3pt}}\\\cline{3-4}\cline{7-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
980\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}&&&\parbox{\wcG}{\vspace{3pt}\noindent
73.5001\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
2.8374\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
76.3375\vspace{3pt}}\\\cline{3-4}\cline{6-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
1120\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}}&&\parbox{\wcF}{\vspace{3pt}\noindent
High confidence\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
186.741\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
5.7\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
181.041\vspace{3pt}}\\\cline{3-3}\cline{6-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
1408\vspace{3pt}}&&&\multirow{2}{*}{\parbox{\wcF}{\vspace{3pt}\noindent
Low confidence\vspace{3pt}}}&\parbox{\wcG}{\vspace{3pt}\noindent
198.342\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
4.304\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
194.038\vspace{3pt}}\\\cline{3-4}\cline{7-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
4514\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
Squared\vspace{3pt}}}&&&\parbox{\wcG}{\vspace{3pt}\noindent
46617.7\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
881.7\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
45736\vspace{3pt}}\\\cline{1-3}\cline{6-9}
\multirow{2}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [source:swissprot;acc:o15120]\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
Divided\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
294\vspace{3pt}}&&&\multirow{2}{*}{\parbox{\wcF}{\vspace{3pt}\noindent
High confidence\vspace{3pt}}}&\parbox{\wcG}{\vspace{3pt}\noindent
30826.5\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.2776\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
39383.9\vspace{3pt}}\\\cline{3-4}\cline{7-9}
&&\parbox{\wcC}{\vspace{3pt}\noindent
508\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Measured\vspace{3pt}}&&&\parbox{\wcG}{\vspace{3pt}\noindent
7556.75\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
1.14293\vspace{3pt}}&\parbox{\wcI}{\vspace{3pt}\noindent
8636.87\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/