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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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 [...,...].
description Gene Network Comparison Type Rank Value Type Filtered Interaction Map red network_comparison green
Results: HTML CSV LaTeX Showing element 51 to 100 of 77072 in total 
Filtered: 1

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description\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
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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{6}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
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74.3877\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
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76.3467\vspace{3pt}}\\\cline{3-4}\cline{6-8}
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1.01914\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
45740.5\vspace{3pt}}\\\cline{2-3}\cline{5-8}
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30826.5\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
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1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [source:swissprot;acc:q9nrz5]\vspace{3pt}}}&\multirow{8}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
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4.7218\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
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1234.6\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
47372.8\vspace{3pt}}\\\cline{1-4}\cline{6-8}
\multirow{16}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [source:swissprot;acc:q9nrz7]\vspace{3pt}}}&\multirow{8}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
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1.27205\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
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1.04731\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
79.1997\vspace{3pt}}\\\cline{3-8}
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1.14143\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
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192.166\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.029\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
186.751\vspace{3pt}}\\\cline{3-8}
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811\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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73.9102\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.06415\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
78.6514\vspace{3pt}}\\\cline{3-4}\cline{6-8}
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187.834\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.03128\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
182.137\vspace{3pt}}\\\cline{3-8}
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4418\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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46049.4\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.02256\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
47088.3\vspace{3pt}}\\\cline{2-4}\cline{6-8}
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526.02\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
9018.94\vspace{3pt}}\\\cline{3-8}
&&\parbox{\wcC}{\vspace{3pt}\noindent
279\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
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8323.7\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
38919.9\vspace{3pt}}\\\cline{3-4}\cline{6-8}
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1058.58\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
8543.66\vspace{3pt}}\\\cline{3-8}
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369\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
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75.6219\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
3.5778\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
79.1997\vspace{3pt}}\\\cline{3-3}\cline{5-8}
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616\vspace{3pt}}&&\parbox{\wcE}{\vspace{3pt}\noindent
High confidence\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
73.9102\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
4.7412\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
78.6514\vspace{3pt}}\\\cline{3-8}
&&\parbox{\wcC}{\vspace{3pt}\noindent
737\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}}&\parbox{\wcE}{\vspace{3pt}\noindent
Low confidence\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
192.166\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
5.415\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
186.751\vspace{3pt}}\\\cline{3-3}\cline{5-8}
&&\parbox{\wcC}{\vspace{3pt}\noindent
1121\vspace{3pt}}&&\parbox{\wcE}{\vspace{3pt}\noindent
High confidence\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
187.834\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
5.697\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
182.137\vspace{3pt}}\\\cline{3-8}
&&\parbox{\wcC}{\vspace{3pt}\noindent
4331\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Squared\vspace{3pt}}&\multirow{5}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
Low confidence\vspace{3pt}}}&\parbox{\wcF}{\vspace{3pt}\noindent
46049.4\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1038.9\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
47088.3\vspace{3pt}}\\\cline{1-4}\cline{6-8}
\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
Divided\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
2035\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Measured\vspace{3pt}}&&\parbox{\wcF}{\vspace{3pt}\noindent
8065.05\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.03199\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
8323.04\vspace{3pt}}\\\cline{3-4}\cline{6-8}
&&\parbox{\wcC}{\vspace{3pt}\noindent
2766\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}&&\parbox{\wcF}{\vspace{3pt}\noindent
72.5914\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.03282\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
74.9741\vspace{3pt}}\\\cline{3-4}\cline{6-8}
&&\parbox{\wcC}{\vspace{3pt}\noindent
3423\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}&&\parbox{\wcF}{\vspace{3pt}\noindent
199.702\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.01523\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
196.707\vspace{3pt}}\\\cline{3-4}\cline{6-8}
&&\parbox{\wcC}{\vspace{3pt}\noindent
3667\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Squared\vspace{3pt}}&&\parbox{\wcF}{\vspace{3pt}\noindent
45400.4\vspace{3pt}}&\parbox{\wcG}{\vspace{3pt}\noindent
1.03124\vspace{3pt}}&\parbox{\wcH}{\vspace{3pt}\noindent
44025.2\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/