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

Results: HTML CSV LaTeX

Showing element 451 to 500 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	Network Comparison Type	description	network_comparison	red	green
57	Ranked	Divided	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	1.25998	266.856	336.233
		Subtracted	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	59.569	185.678	245.247
	Squared	Divided	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	1.68808	219048	129762
		Subtracted	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	69581	173408	242989
	Rooted	Divided	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]	1.43973	41.6879	28.9554
		Subtracted	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	16.623	137.446	120.823
58	Measured	Divided	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]	1.63302	1631.67	2664.55
		Subtracted	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	3997.5	20911	24908.5
	Ranked	Divided	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	1.25979	266.863	336.191
		Subtracted	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	59.569	185.678	245.247
	Squared	Divided	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	1.68808	219048	129762
		Subtracted	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	69581	173408	242989
	Rooted	Divided	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	1.43933	41.6969	28.9696
		Subtracted	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	16.623	137.446	120.823
59	Measured	Divided	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	1.63302	1631.67	2664.55
		Subtracted	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]	3997.5	20911	24908.5
	Ranked	Divided	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	1.25978	266.863	336.19
		Subtracted	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	58.431	269.278	327.709
	Squared	Divided	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	1.68808	219048	129762
		Subtracted	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873]	69573	199594	130021
	Rooted	Divided	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09]	1.40262	37.2205	52.2064
		Subtracted	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	16.623	137.446	120.823
60	Measured	Divided	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	1.6231	4489.19	2765.82
		Subtracted	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	3882.4	16771.5	12889.1
	Ranked	Divided	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	1.25976	266.864	336.184
		Subtracted	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	58.401	269.254	327.655
	Squared	Divided	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	1.68808	219048	129762
		Subtracted	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	66737	192904	126167
	Rooted	Divided	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	1.39806	35.6294	49.8119
		Subtracted	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	16.623	137.446	120.823
61	Measured	Divided	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	1.6231	4489.19	2765.82
		Subtracted	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	3832	6475.5	10307.5
	Ranked	Divided	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	1.25975	266.864	336.182
		Subtracted	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]	58.394	269.248	327.642
	Squared	Divided	necdin. [swissprot;acc:q99608]	1.68808	219048	129762
		Subtracted	type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210]	66684	192779	126095
	Rooted	Divided	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	1.36932	43.4291	31.7159
		Subtracted	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	16.623	137.446	120.823
62	Measured	Divided	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	1.6231	4489.19	2765.82
		Subtracted	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	3832	6475.5	10307.5
	Ranked	Divided	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	1.25974	266.865	336.181
		Subtracted	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	58.371	269.23	327.601
	Squared	Divided	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	1.68808	219048	129762
		Subtracted	ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050]	65496	189976	124480
	Rooted	Divided	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	1.36847	43.4519	31.7522
		Subtracted	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	16.623	137.446	120.823
63	Measured	Divided	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	1.6231	4489.19	2765.82
		Subtracted	spermatogenesis associated 6. [refseq;acc:nm_019073]	3832	6475.5	10307.5
	Ranked	Divided	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	1.25973	266.865	336.178
		Subtracted	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]	56.223	260.532	204.309

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.