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

Results: HTML CSV LaTeX

Showing element 501 to 550 of 38536 in total

Network Comparison Type  : Divided

Rank	description	Filtered	Interaction Map	Value Type	green	red	network_comparison
32	importin 9. [refseq;acc:nm_018085]	0	High confidence	Ranked	8691.76	13292.2	1.52929
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]		Low confidence	Rooted	5.80678	9.84765	1.69589
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	1		Squared	61881.5	82347.8	1.33073
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	0		Measured	35.5	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]	1		Rooted	168.796	145.551	1.1597
	myoglobin. [swissprot;acc:p02144]	0		Ranked	15983.3	11485.4	1.39162
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	1		Measured	43368.8	36360.3	1.19275
	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	0	High confidence	Squared	4.57302	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]	1	Low confidence	Ranked	232.49	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]		High confidence		243.673	187.462	1.29985
	ubiquitin protein ligase. [refseq;acc:nm_130466]	0		Rooted	11.258	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]	1	Low confidence	Ranked	246.125	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]	0	High confidence	Rooted	25.7294	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]		Low confidence	Ranked	14746.1	20324.1	1.37827
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	1	High confidence	Measured	896.972	1835.3	2.04611
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]		Low confidence	Squared	61881.5	82347.8	1.33073
	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	0	High confidence	Measured	39.8063	12.6208	3.15402
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]		Low confidence	Rooted	5.80678	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]		High confidence	Ranked	8691.76	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]	1		Rooted	43.1914	26.0288	1.65937
	retinoblastoma-associated factor 600. [refseq;acc:nm_020765]		Low confidence		88.6244	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]		High confidence	Ranked	242.742	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]		Low confidence	Measured	43368.8	36360.3	1.19275
34	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]		High confidence	Squared	25146.6	9924.76	2.53372
	fibrillin 3. [refseq;acc:nm_032447]	0	Low confidence	Ranked	7506.66	5450.5	1.37724
	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]		High confidence	Measured	47	143	3.04255
	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	1			907.546	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]	0		Squared	0.697197	0.0435834	15.9968
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]		Low confidence	Rooted	5.80678	9.84765	1.69589
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	1		Squared	61881.5	82347.8	1.33073
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	0			0.355148	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]		High confidence	Ranked	17173.8	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]	1	Low confidence	Measured	6352.4	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]		High confidence	Ranked	242.453	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]	0		Measured	1377	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]	1	Low confidence	Measured	39358.1	33111.4	1.18866
	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]		High confidence		907.564	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.