MK5 Microarray Data

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

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Showing element 451 to 500 of 6456 in total

Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence

description	Network Comparison Type	Rank	red	network_comparison	green
adp-ribosylation factor 1. [swissprot;acc:p32889]	Divided	2128	221.248	1.00696	222.788
	Subtracted	2110		1.54
adp-ribosylation factor 3. [swissprot;acc:p16587]	Divided	2130		1.00696
	Subtracted	2112		1.54
adp-ribosylation factor 4. [swissprot;acc:p18085]	Divided	2123		1.00696
	Subtracted	2105		1.54
adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3]	Divided	2156	200.063	1.00681	198.71
	Subtracted	2219		1.353
adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Divided	2137	221.248	1.00696	222.788
	Subtracted	2116		1.54
adp-ribosylation factor-like protein 1. [swissprot;acc:p40616]	Divided	2613	215.497	1.0014	215.799
	Subtracted	2623		0.302
adp-ribosylation factor-like protein 3. [swissprot;acc:p36405]	Divided	2520	215.835	1.00234	216.341
	Subtracted	2517		0.506
adp-ribosylation factor-like protein 4. [swissprot;acc:p40617]	Divided	1188	218.402	1.02582	212.904
	Subtracted	1163		5.498
adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	Divided	1186		1.02582
	Subtracted	1161		5.498
adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109]	Divided	1105	191.139	1.02828	185.882
	Subtracted	1226		5.257
af-6 protein. [swissprot;acc:p55196]	Divided	1530	218.733	1.01746	214.98
	Subtracted	1528		3.753
afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6]	Divided	1725	217.676	1.01311	220.53
	Subtracted	1709		2.854
aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488]	Divided	1969	211.633	1.00978	213.703
	Subtracted	1938		2.07
aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154]	Divided	1958		1.00978
	Subtracted	1928		2.07
ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170]	Divided	1157	224.307	1.02646	230.242
	Subtracted	1075		5.935
alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]	Divided	2025	189.987	1.00885	191.668
	Subtracted	2078		1.681
alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443]	Divided	2030	189.999	1.00883	191.677
	Subtracted	2081		1.678
alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588]	Divided	633	234.106	1.05979	248.104
	Subtracted	547		13.998
alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766]	Divided	2428	192.871	1.00355	193.555
	Subtracted	2445		0.684
aldehyde dehydrogenase 7 (ec 1.2.1.5). [swissprot;acc:p43353]	Divided	3222	0.00001	1	0.00001
	Subtracted		0	0	0
aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]	Divided	2992	0.00001	1	0.00001
	Subtracted		0	0	0
aldehyde oxidase (ec 1.2.3.1). [swissprot;acc:q06278]	Divided	2960	0.00001	1	0.00001
	Subtracted		0	0	0
alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611]	Divided	1965	224.432	1.00978	222.258
	Subtracted	1908		2.174
alpha crystallin a chain. [swissprot;acc:p02489]	Divided	2875	0.00001	1	0.00001
	Subtracted		0	0	0
alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511]	Divided	3082	0.00001	1	0.00001
	Subtracted		0	0	0

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.