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	Rank	Gene	Value Type	Interaction Map	Filtered	green	Network Comparison Type	red	network_comparison

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Showing element 551 to 600 of 6456 in total

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

description	Rank	green	Network Comparison Type	red	network_comparison
anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	2636	195.384	Divided	195.635	1.00128
	2639		Subtracted		0.251
anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885]	2663	204.549	Divided	204.768	1.00107
	2667		Subtracted		0.219
anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366]	2679	189.959	Divided	190.142	1.00096
	2682		Subtracted		0.183
androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]	184	254.15		227.357	26.793
	240		Divided		1.11785
angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [refseq;acc:nm_016201]	2586	213.75		213.422	1.00154
			Subtracted		0.328
angiomotin. [refseq;acc:nm_133265]	2585		Divided		1.00154
			Subtracted		0.328
anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]	143	49	Divided	59	1.20408
	773		Subtracted		10
ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484]	2516	216.341		215.835	0.506
	2519		Divided		1.00234
ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955]	2515		Subtracted		0.506
	2518		Divided		1.00234
ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1]	793	221.785	Subtracted	212.386	9.399
	805		Divided		1.04425
annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995]	1051	213.378	Subtracted	219.673	6.295
	1088		Divided		1.0295
annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073]	1053	213.385	Subtracted	219.655	6.27
	1094		Divided		1.02938
antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008]	2406	218.984	Subtracted	218.2	0.784
	2418		Divided		1.00359
apg3p; pc3-96 protein. [refseq;acc:nm_022488]	169	98.0548		82.5916	1.18722
	489		Subtracted		15.4632
apical-like protein (apxl protein). [swissprot;acc:q13796]	346	211.136		231.492	20.356
	362		Divided		1.09641
apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]	211	212.41	Subtracted	237.302	24.892
	248		Divided		1.11719
apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772]	1606	204.662		207.916	1.0159
	1609		Subtracted		3.254
apolipoprotein b-100 precursor (apo b-100) [contains: apolipoprotein b-48 (apo b-48)]. [swissprot;acc:p04114]	2128	219.366		217.871	1.495
	2151		Divided		1.00686
apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [swissprot;acc:p42574]	1166	228.46	Subtracted	233.942	5.482
	1293		Divided		1.024
apoptosis antagonizing transcription factor. [refseq;acc:nm_012138]	929	235.422	Subtracted	243.045	7.623
	1014		Divided		1.03238
apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]	1094	212.675	Subtracted	218.484	5.809
	1132		Divided		1.02731
apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	1083	212.123	Subtracted	217.99	5.867
	1111		Divided		1.02766
apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797]	2418	209.454	Subtracted	210.205	0.751
	2421		Divided		1.00359
apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481]	2523	215.787	Subtracted	216.264	0.477
	2531		Divided		1.00221
aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087]	2688	188.046	Subtracted	188.191	0.145
	2690		Divided		1.00077

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.