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

Results: HTML CSV LaTeX

Showing element 551 to 600 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	Network Comparison Type	description	network_comparison	red	green
69	Rooted	Divided	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	1.33581	27.9136	37.2872
		Subtracted	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	16.6032	63.8686	47.2654
70	Measured	Divided	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	1.59177	6475.5	10307.5
		Subtracted	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537]	3742.8	17738.5	13995.7
	Ranked	Divided	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]	1.25804	267.142	336.074
		Subtracted	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]	54.054	188.688	242.742
	Squared	Divided	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	1.68808	219048	129762
		Subtracted	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	56439.5	129597	73157.5
	Rooted	Divided	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	1.33581	27.9136	37.2872
		Subtracted	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	16.6032	63.8686	47.2654
71	Measured	Divided	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007]	1.54716	4556.78	2945.26
		Subtracted	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172]	3742.8	17738.5	13995.7
	Ranked	Divided	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]	1.25802	267.144	336.073
		Subtracted	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	53.965	265.686	319.651
	Squared	Divided	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	1.68808	219048	129762
		Subtracted	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	56439.5	129597	73157.5
	Rooted	Divided	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	1.33581	27.9136	37.2872
		Subtracted	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	16.6032	63.8686	47.2654
72	Measured	Divided	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	1.54715	4556.79	2945.28
		Subtracted	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]	3733.2	17710.9	13977.7
	Ranked	Divided	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]	1.25802	267.144	336.073
		Subtracted	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	53.907	265.639	319.546
	Squared	Divided	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	1.68808	219048	129762
		Subtracted	44050 protein. [refseq;acc:nm_178832]	48429.6	148058	99628.4
	Rooted	Divided	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	1.33581	27.9136	37.2872
		Subtracted	deltex 2. [refseq;acc:nm_020892]	16.3289	27.634	43.9629
73	Measured	Divided	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005]	1.54711	4556.83	2945.38
		Subtracted	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873]	3708.4	22268.8	18560.4
	Ranked	Divided	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	1.25694	288	362
		Subtracted	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]	53.899	265.632	319.531
	Squared	Divided	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	1.68808	219048	129762
		Subtracted	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972]	48429.6	148058	99628.4
	Rooted	Divided	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	1.33581	27.9136	37.2872
		Subtracted	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	16.3092	27.7078	44.017
74	Measured	Divided	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]	1.54694	4556.99	2945.8
		Subtracted	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	3690.3	20446.1	24136.4
	Ranked	Divided	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	1.25694	288	362
		Subtracted	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]	53.383	189.07	242.453
	Squared	Divided	trophinin. [swissprot;acc:q12816]	1.68808	219048	129762
		Subtracted	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	47287.9	117858	70570.1
	Rooted	Divided	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	1.33581	27.9136	37.2872
		Subtracted	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	16.3045	27.7254	44.0299
75	Measured	Divided	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181]	1.5137	1920.75	2907.43
		Subtracted	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	3690.3	20446.1	24136.4
	Ranked	Divided	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	1.25694	288	362
		Subtracted	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	52.025	254.693	202.668
	Squared	Divided	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	1.67024	110342	184298
		Subtracted	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	47283.2	117850	70566.8
	Rooted	Divided	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	1.33581	27.9136	37.2872
		Subtracted	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	16.3045	27.7254	44.0299

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.