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

Results: HTML CSV LaTeX

Showing element 425 to 474 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	description	Network Comparison Type	red	green	network_comparison
54	Measured	deltex 2. [refseq;acc:nm_020892]	Divided	1618.84	2651.88	1.63814
		exocyst complex component sec5. [swissprot;acc:q96kp1]	Subtracted	23316	19288.8	4027.2
	Ranked	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]		185.678	245.247	59.569
		transcription factor jun-d. [swissprot;acc:p17535]	Divided	200.941	158.941	1.26425
	Squared	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	Subtracted	173408	242989	69581
		melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Divided	219048	129762	1.68808
	Rooted	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Subtracted	137.446	120.823	16.623
		protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Divided	40.0958	58.7986	1.46645
55	Measured	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]		1629.21	2662.12	1.63399
		poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	Subtracted	23303.1	19279.5	4023.6
	Ranked	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]		185.678	245.247	59.569
		protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Divided	320.927	254.434	1.26134
	Squared	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]		219048	129762	1.68808
		homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]	Subtracted	173408	242989	69581
	Rooted	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]		137.446	120.823	16.623
		potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Divided	41.6734	28.9323	1.44038
56	Measured	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Subtracted	20911	24908.5	3997.5
		t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	Divided	1631.67	2664.55	1.63302
	Ranked	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	Subtracted	185.678	245.247	59.569
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Divided	266.856	336.233	1.25998
	Squared	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	Subtracted	173408	242989	69581
		melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Divided	219048	129762	1.68808
	Rooted	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]		41.6851	28.9509	1.43986
		melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Subtracted	137.446	120.823	16.623
57	Measured	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	Divided	1631.67	2664.55	1.63302
		ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Subtracted	20911	24908.5	3997.5
	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	Divided	266.856	336.233	1.25998
		myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	Subtracted	185.678	245.247	59.569
	Squared	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]		173408	242989	69581
		melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Divided	219048	129762	1.68808
	Rooted	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Subtracted	137.446	120.823	16.623
		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]	Divided	41.6879	28.9554	1.43973
58	Measured	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]		1631.67	2664.55	1.63302
		ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Subtracted	20911	24908.5	3997.5
	Ranked	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]		185.678	245.247	59.569
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Divided	266.863	336.191	1.25979
	Squared	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]		219048	129762	1.68808
		retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Subtracted	173408	242989	69581
	Rooted	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]		137.446	120.823	16.623
		potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	Divided	41.6969	28.9696	1.43933
59	Measured	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]	Subtracted	20911	24908.5	3997.5
		kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	Divided	1631.67	2664.55	1.63302
	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]		266.863	336.19	1.25978
		potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Subtracted	269.278	327.709	58.431
	Squared	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Divided	219048	129762	1.68808
		serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873]	Subtracted	199594	130021	69573
	Rooted	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]		137.446	120.823	16.623
		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]	Divided	37.2205	52.2064	1.40262
60	Measured	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]		4489.19	2765.82	1.6231
		ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Subtracted	16771.5	12889.1	3882.4

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.