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	description	Filtered	green	Network Comparison Type	network_comparison	Interaction Map	red

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Showing element 501 to 550 of 38536 in total

Network Comparison Type  : Divided

Rank	Value Type	description	Filtered	green	network_comparison	Interaction Map	red
32	Ranked	importin 9. [refseq;acc:nm_018085]	0	8691.76	1.52929	High confidence	13292.2
		myoglobin. [swissprot;acc:p02144]		15983.3	1.39162	Low confidence	11485.4
		protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	1	232.49	1.17505		273.188
		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]		243.673	1.29985	High confidence	187.462
	Squared	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]		25146.6	2.53372		9924.76
		melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]		61881.5	1.33073	Low confidence	82347.8
		melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	0	0.355148	9.62112		3.41692
		phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]		4.57302	16.8159	High confidence	76.8994
	Rooted	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	1	43.1914	1.65937		26.0288
		melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	0	5.80678	1.69589	Low confidence	9.84765
		mitochondrial solute carrier protein. [refseq;acc:nm_145305]	1	168.796	1.1597		145.551
		ubiquitin protein ligase. [refseq;acc:nm_130466]	0	11.258	2.13529	High confidence	24.0391
33	Measured	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	1	896.972	2.04611		1835.3
		lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	0	39.8063	3.15402		12.6208
		melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]		35.5	2.97183	Low confidence	105.5
		vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]	1	43368.8	1.19275		36360.3
	Ranked	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]		246.125	1.17068		210.241
		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]	0	14746.1	1.37827		20324.1
		nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]		8691.76	1.52929	High confidence	13292.2
		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]	1	242.742	1.28647		188.688
	Squared	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	0	4.57302	16.8159		76.8994
		hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	1	61881.5	1.33073	Low confidence	82347.8
		melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	0	0.355148	9.62112		3.41692
		spermatogenesis associated 6. [refseq;acc:nm_019073]	1	25146.6	2.53372	High confidence	9924.76
	Rooted	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	0	25.7294	2.0801		12.3693
		melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]		5.80678	1.69589	Low confidence	9.84765
		protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	1	43.1914	1.65937	High confidence	26.0288
		retinoblastoma-associated factor 600. [refseq;acc:nm_020765]		88.6244	1.15738	Low confidence	76.5734
34	Measured	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	0	47	3.04255	High confidence	143
		guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	1	907.546	2.02382		1836.71
		melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	0	35.5	2.97183	Low confidence	105.5
		protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	1	6352.4	1.1897		5339.5
	Ranked	fibrillin 3. [refseq;acc:nm_032447]	0	7506.66	1.37724		5450.5
		microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]		17173.8	1.52196	High confidence	11284
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	1	133.876	1.16197	Low confidence	155.56
		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]		242.453	1.28235	High confidence	189.07
	Squared	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]		25146.6	2.53372		9924.76
		lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	0	0.697197	15.9968		0.0435834
		melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	1	61881.5	1.33073	Low confidence	82347.8
		melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	0	0.355148	9.62112		3.41692
	Rooted	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	1	24.3678	1.65305	High confidence	40.2812
		melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	0	5.80678	1.69589	Low confidence	9.84765
		phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]		11.7898	2.02503	High confidence	23.8747
		putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580]	1	56.755	1.15698	Low confidence	49.0544
35	Measured	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	0	1377	2.99674	High confidence	459.5
		deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	1	39358.1	1.18866	Low confidence	33111.4
		guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]		907.564	2.02378	High confidence	1836.71
		melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	0	35.5	2.97183	Low confidence	105.5
	Ranked	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		4871.6	1.5182	High confidence	3208.8
		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]	1	204.309	1.27519		260.532

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.