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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 501 to 550 of 38536 in total

Network Comparison Type  : Divided

Rank	Filtered	Interaction Map	green	network_comparison	description	Value Type	red
32	0	Low confidence	0.355148	9.62112	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Squared	3.41692
			5.80678	1.69589	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Rooted	9.84765
			35.5	2.97183	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Measured	105.5
			15983.3	1.39162	myoglobin. [swissprot;acc:p02144]	Ranked	11485.4
	1	High confidence	43.1914	1.65937	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Rooted	26.0288
			243.673	1.29985	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]	Ranked	187.462
			895.893	2.04793	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Measured	1834.73
			25146.6	2.53372	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Squared	9924.76
		Low confidence	168.796	1.1597	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Rooted	145.551
			232.49	1.17505	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Ranked	273.188
			43368.8	1.19275	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Measured	36360.3
			61881.5	1.33073	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Squared	82347.8
33	0	High confidence	4.57302	16.8159	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]		76.8994
			25.7294	2.0801	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	12.3693
			39.8063	3.15402	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	Measured	12.6208
			8691.76	1.52929	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	Ranked	13292.2
		Low confidence	0.355148	9.62112	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Squared	3.41692
			5.80678	1.69589	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Rooted	9.84765
			35.5	2.97183	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Measured	105.5
			14746.1	1.37827	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
	1	High confidence	43.1914	1.65937	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	26.0288
			242.742	1.28647	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
			896.972	2.04611	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	Measured	1835.3
			25146.6	2.53372	spermatogenesis associated 6. [refseq;acc:nm_019073]	Squared	9924.76
		Low confidence	88.6244	1.15738	retinoblastoma-associated factor 600. [refseq;acc:nm_020765]	Rooted	76.5734
			246.125	1.17068	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	210.241
			43368.8	1.19275	vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]	Measured	36360.3
			61881.5	1.33073	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Squared	82347.8
34	0	High confidence	0.697197	15.9968	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]		0.0435834
			11.7898	2.02503	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	Rooted	23.8747
			47	3.04255	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	Measured	143
			17173.8	1.52196	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	Ranked	11284
		Low confidence	0.355148	9.62112	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	Squared	3.41692
			5.80678	1.69589	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Rooted	9.84765
			35.5	2.97183	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Measured	105.5
			7506.66	1.37724	fibrillin 3. [refseq;acc:nm_032447]	Ranked	5450.5
	1	High confidence	24.3678	1.65305	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	Rooted	40.2812
			242.453	1.28235	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
			907.546	2.02382	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	Measured	1836.71
			25146.6	2.53372	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	Squared	9924.76
		Low confidence	56.755	1.15698	putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580]	Rooted	49.0544
			133.876	1.16197	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Ranked	155.56
			6352.4	1.1897	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Measured	5339.5
			61881.5	1.33073	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Squared	82347.8
35	0	High confidence	11.7898	2.02503	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Rooted	23.8747
			647.816	12.7767	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	Squared	50.7031
			1377	2.99674		Measured	459.5
			4871.6	1.5182	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Ranked	3208.8
		Low confidence	0.355148	9.62112	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Squared	3.41692
			5.80678	1.69589	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Rooted	9.84765

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.