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

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Showing element 501 to 550 of 38536 in total

Network Comparison Type  : Divided

Rank	description	Value Type	Filtered	red	green	Interaction Map	network_comparison
32	importin 9. [refseq;acc:nm_018085]	Ranked	0	13292.2	8691.76	High confidence	1.52929
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Rooted		9.84765	5.80678	Low confidence	1.69589
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Squared	1	82347.8	61881.5		1.33073
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Measured	0	105.5	35.5		2.97183
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Squared		3.41692	0.355148		9.62112
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Rooted	1	145.551	168.796		1.1597
	myoglobin. [swissprot;acc:p02144]	Ranked	0	11485.4	15983.3		1.39162
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Measured	1	36360.3	43368.8		1.19275
	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	Squared	0	76.8994	4.57302	High confidence	16.8159
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Ranked	1	273.188	232.49	Low confidence	1.17505
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4]			187.462	243.673	High confidence	1.29985
	ubiquitin protein ligase. [refseq;acc:nm_130466]	Rooted	0	24.0391	11.258		2.13529
33	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Squared		76.8994	4.57302		16.8159
	dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985]	Ranked	1	210.241	246.125	Low confidence	1.17068
	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Rooted	0	12.3693	25.7294	High confidence	2.0801
	fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344]	Ranked		20324.1	14746.1	Low confidence	1.37827
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	Measured	1	1835.3	896.972	High confidence	2.04611
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Squared		82347.8	61881.5	Low confidence	1.33073
	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	Measured	0	12.6208	39.8063	High confidence	3.15402
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Rooted		9.84765	5.80678	Low confidence	1.69589
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Squared		3.41692	0.355148		9.62112
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Measured		105.5	35.5		2.97183
	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	Ranked		13292.2	8691.76	High confidence	1.52929
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Rooted	1	26.0288	43.1914		1.65937
	retinoblastoma-associated factor 600. [refseq;acc:nm_020765]			76.5734	88.6244	Low confidence	1.15738
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]	Ranked		188.688	242.742	High confidence	1.28647
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Squared		9924.76	25146.6		2.53372
	vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]	Measured		36360.3	43368.8	Low confidence	1.19275
34	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	Squared		9924.76	25146.6	High confidence	2.53372
	fibrillin 3. [refseq;acc:nm_032447]	Ranked	0	5450.5	7506.66	Low confidence	1.37724
	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	Measured		143	47	High confidence	3.04255
	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]		1	1836.71	907.546		2.02382
		Rooted		40.2812	24.3678		1.65305
	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	Squared	0	0.0435834	0.697197		15.9968
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Rooted		9.84765	5.80678	Low confidence	1.69589
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Squared	1	82347.8	61881.5		1.33073
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]		0	3.41692	0.355148		9.62112
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Measured		105.5	35.5		2.97183
	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	Ranked		11284	17173.8	High confidence	1.52196
	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	Rooted		23.8747	11.7898		2.02503
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Measured	1	5339.5	6352.4	Low confidence	1.1897
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Ranked		155.56	133.876		1.16197
	putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580]	Rooted		49.0544	56.755		1.15698
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]	Ranked		189.07	242.453	High confidence	1.28235
35	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Squared		106226	192141		1.80879
	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	Measured	0	459.5	1377		2.99674
		Squared		50.7031	647.816		12.7767
	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Rooted		23.8747	11.7898		2.02503
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Measured	1	33111.4	39358.1	Low confidence	1.18866
	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]			1836.71	907.564	High confidence	2.02378

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.