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	green	Filtered	Interaction Map	red	network_comparison

Results: HTML CSV LaTeX

Showing element 501 to 550 of 38536 in total

Network Comparison Type  : Divided

Rank	description	Value Type	green	Filtered	Interaction Map	red	network_comparison
32	importin 9. [refseq;acc:nm_018085]	Ranked	8691.76	0	High confidence	13292.2	1.52929
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Rooted	5.80678		Low confidence	9.84765	1.69589
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Squared	61881.5	1		82347.8	1.33073
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Measured	35.5	0		105.5	2.97183
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Squared	0.355148			3.41692	9.62112
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Rooted	168.796	1		145.551	1.1597
	myoglobin. [swissprot;acc:p02144]	Ranked	15983.3	0		11485.4	1.39162
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Measured	43368.8	1		36360.3	1.19275
	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	Squared	4.57302	0	High confidence	76.8994	16.8159
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Ranked	232.49	1	Low confidence	273.188	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]		243.673		High confidence	187.462	1.29985
	ubiquitin protein ligase. [refseq;acc:nm_130466]	Rooted	11.258	0		24.0391	2.13529
33	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Squared	4.57302			76.8994	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	246.125	1	Low confidence	210.241	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	25.7294	0	High confidence	12.3693	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	14746.1		Low confidence	20324.1	1.37827
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	Measured	896.972	1	High confidence	1835.3	2.04611
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Squared	61881.5		Low confidence	82347.8	1.33073
	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	Measured	39.8063	0	High confidence	12.6208	3.15402
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Rooted	5.80678		Low confidence	9.84765	1.69589
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Squared	0.355148			3.41692	9.62112
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Measured	35.5			105.5	2.97183
	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	Ranked	8691.76		High confidence	13292.2	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	43.1914	1		26.0288	1.65937
	retinoblastoma-associated factor 600. [refseq;acc:nm_020765]		88.6244		Low confidence	76.5734	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	242.742		High confidence	188.688	1.28647
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Squared	25146.6			9924.76	2.53372
	vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]	Measured	43368.8		Low confidence	36360.3	1.19275
34	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	Squared	25146.6		High confidence	9924.76	2.53372
	fibrillin 3. [refseq;acc:nm_032447]	Ranked	7506.66	0	Low confidence	5450.5	1.37724
	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	Measured	47		High confidence	143	3.04255
	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]		907.546	1		1836.71	2.02382
		Rooted	24.3678			40.2812	1.65305
	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	Squared	0.697197	0		0.0435834	15.9968
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Rooted	5.80678		Low confidence	9.84765	1.69589
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Squared	61881.5	1		82347.8	1.33073
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]		0.355148	0		3.41692	9.62112
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Measured	35.5			105.5	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	17173.8		High confidence	11284	1.52196
	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	Rooted	11.7898			23.8747	2.02503
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Measured	6352.4	1	Low confidence	5339.5	1.1897
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Ranked	133.876			155.56	1.16197
	putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580]	Rooted	56.755			49.0544	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	242.453		High confidence	189.07	1.28235
35	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Squared	192141			106226	1.80879
	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	Measured	1377	0		459.5	2.99674
		Squared	647.816			50.7031	12.7767
	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Rooted	11.7898			23.8747	2.02503
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Measured	39358.1	1	Low confidence	33111.4	1.18866
	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]		907.564		High confidence	1836.71	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.