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	red	Network Comparison Type	Interaction Map	Filtered	network_comparison	green

Results: HTML CSV LaTeX

Showing element 551 to 600 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	red	Network Comparison Type	network_comparison	green
69	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	Squared	178263	Subtracted	59624	118639
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Measured	6475.5	Divided	1.59177	10307.5
70	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	Rooted	27.9136		1.33581	37.2872
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Squared	129597	Subtracted	56439.5	73157.5
	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]	Ranked	267.142	Divided	1.25804	336.074
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Squared	219048		1.68808	129762
	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	Rooted	63.8686	Subtracted	16.6032	47.2654
	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]	Measured	17738.5		3742.8	13995.7
	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		54.054	242.742
71	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	Squared	129597		56439.5	73157.5
	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	Rooted	27.9136	Divided	1.33581	37.2872
	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]		63.8686	Subtracted	16.6032	47.2654
	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]	Ranked	267.144	Divided	1.25802	336.073
	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]		265.686	Subtracted	53.965	319.651
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Squared	219048	Divided	1.68808	129762
	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]	Measured	4556.78		1.54716	2945.26
	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]		17738.5	Subtracted	3742.8	13995.7
72	44050 protein. [refseq;acc:nm_178832]	Squared	148058		48429.6	99628.4
	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]	Measured	17710.9		3733.2	13977.7
	deltex 2. [refseq;acc:nm_020892]	Rooted	27.634		16.3289	43.9629
	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]	Ranked	267.144	Divided	1.25802	336.073
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Squared	219048		1.68808	129762
	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Rooted	27.9136		1.33581	37.2872
	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	Ranked	265.639	Subtracted	53.907	319.546
	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	Measured	4556.79	Divided	1.54715	2945.28
73	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Rooted	27.7078	Subtracted	16.3092	44.017
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Ranked	288	Divided	1.25694	362
	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]		265.632	Subtracted	53.899	319.531
	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]	Squared	219048	Divided	1.68808	129762
	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	Rooted	27.9136		1.33581	37.2872
	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]	Squared	148058	Subtracted	48429.6	99628.4
	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]	Measured	4556.83	Divided	1.54711	2945.38
	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873]		22268.8	Subtracted	3708.4	18560.4
74	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	Squared	117858		47287.9	70570.1
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Measured	20446.1		3690.3	24136.4
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Ranked	288	Divided	1.25694	362
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Rooted	27.9136		1.33581	37.2872
	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]	Measured	4556.99		1.54694	2945.8
	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	Subtracted	53.383	242.453
	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]	Rooted	27.7254		16.3045	44.0299
	trophinin. [swissprot;acc:q12816]	Squared	219048	Divided	1.68808	129762
75	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Rooted	27.9136		1.33581	37.2872
	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	Measured	20446.1	Subtracted	3690.3	24136.4
	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	Rooted	27.7254		16.3045	44.0299
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Squared	110342	Divided	1.67024	184298
	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]	Measured	1920.75		1.5137	2907.43
	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	Squared	117850	Subtracted	47283.2	70566.8
	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]	Ranked	288	Divided	1.25694	362
	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]		254.693	Subtracted	52.025	202.668

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.