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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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

Results: HTML CSV LaTeX

Showing element 508 to 557 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Hugo	description	Network Comparison Type	Value Type	red	green	network_comparison
64	GNG11	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	Divided	Ranked	266.868	336.159	1.25965
	MAGEB4	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Subtracted	Rooted	137.446	120.823	16.623
	MAGEB6B	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Divided	Squared	219048	129762	1.68808
	NFYA	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]	Subtracted	Ranked	260.532	204.309	56.223
	PYGM	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	Divided	Measured	4489.19	2765.82	1.6231
65	no value	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]		Squared	219048	129762	1.68808
		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]	Subtracted	Ranked	187.457	243.678	56.221
	CSTF3	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]		Measured	22515.5	18702.6	3812.9
	GNAQ	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	Divided	Ranked	267.136	336.077	1.25807
	MAGED2	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]	Subtracted	Rooted	137.446	120.823	16.623
	MAP1LC3B	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]		Squared	144912	81155	63757
	NEURL	neuralized-like. [refseq;acc:nm_004210]	Divided	Measured	1657.68	2690.25	1.6229
	PYGB	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]		Rooted	63.8686	47.2654	1.35128
66	ARAF	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	Subtracted	Measured	17757.5	14008	3749.5
	GNA11	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	Divided	Ranked	267.136	336.077	1.25807
	MAGEA9	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]		Squared	219048	129762	1.68808
	MAP1LC3A	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	Subtracted		144911	81154.7	63756.3
	NDUFA12	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09]	Divided	Measured	1991.03	3221.38	1.61795
	PPP2R2D	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	Subtracted	Ranked	187.458	243.678	56.22
	PYGL	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	Divided	Rooted	63.8686	47.2654	1.35128
	TRO	trophinin. [swissprot;acc:q12816]	Subtracted		137.446	120.823	16.623
67	ARRB2	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Divided	Measured	6475.5	10307.5	1.59177
	ATG4B	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Subtracted	Squared	144876	81136.5	63739.5
	GBE1	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]		Rooted	63.8686	47.2654	16.6032
	GNAT2	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	Divided	Ranked	267.14	336.075	1.25805
	MAGEA8	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]		Squared	219048	129762	1.68808
	MYO15A	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]		Rooted	63.8686	47.2654	1.35128
	PPP2R2B	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]	Subtracted	Ranked	187.458	243.677	56.219
	RAF1	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]		Measured	17756.5	14007.3	3749.2
68	ARRB1	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Divided		6475.5	10307.5	1.59177
	CCNG2	cyclin g2. [swissprot;acc:q16589]	Subtracted		17738.6	13995.7	3742.9
	GABARAP	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]		Squared	139741	78454.6	61286.4
	GNAZ	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	Divided	Ranked	267.139	336.075	1.25805
	MAGEC1	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]		Squared	219048	129762	1.68808
	PPP2R2C	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]	Subtracted	Ranked	187.462	243.673	56.211
	PYGB	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]		Rooted	63.8686	47.2654	16.6032
	PYGM	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	Divided				1.35128
69	CCNG1	cyclin g1 (cyclin g). [swissprot;acc:p51959]	Subtracted	Measured	17738.5	13995.6	3742.9
	GNAT1	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	Divided	Ranked	267.14	336.075	1.25805
	MAGEA4	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]		Squared	219048	129762	1.68808
	NDUFA12	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09]	Subtracted	Ranked	284.753	228.934	55.819
	NEUROD2	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	Divided	Rooted	27.9136	37.2872	1.33581
	PCF11	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	Subtracted	Squared	178263	118639	59624
	PYGL	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]		Rooted	63.8686	47.2654	16.6032
	SPATA6	spermatogenesis associated 6. [refseq;acc:nm_019073]	Divided	Measured	6475.5	10307.5	1.59177
70	no value	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Subtracted	Squared	129597	73157.5	56439.5
		melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Divided		219048	129762	1.68808
	AMPD2	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]		Measured	6475.5	10307.5	1.59177
	CHD3	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]		Rooted	27.9136	37.2872	1.33581
	GNAI2	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]		Ranked	267.142	336.074	1.25804

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
- Hugo is the HGNC identifier if it exists
- 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.