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

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Showing element 512 to 561 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Hugo	Value Type	Network Comparison Type	red	network_comparison	green
64	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	MAGEB4	Rooted	Subtracted	137.446	16.623	120.823
65	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	CSTF3	Measured		22515.5	3812.9	18702.6
	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	PYGB	Rooted	Divided	63.8686	1.35128	47.2654
	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	GNAQ	Ranked		267.136	1.25807	336.077
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	no value	Squared		219048	1.68808	129762
	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]	MAGED2	Rooted	Subtracted	137.446	16.623	120.823
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	MAP1LC3B	Squared		144912	63757	81155
	neuralized-like. [refseq;acc:nm_004210]	NEURL	Measured	Divided	1657.68	1.6229	2690.25
	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]	no value	Ranked	Subtracted	187.457	56.221	243.678
66	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	ARAF	Measured		17757.5	3749.5	14008
	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	PYGL	Rooted	Divided	63.8686	1.35128	47.2654
	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	GNA11	Ranked		267.136	1.25807	336.077
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	MAGEA9	Squared		219048	1.68808	129762
	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	MAP1LC3A		Subtracted	144911	63756.3	81154.7
	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]	NDUFA12	Measured	Divided	1991.03	1.61795	3221.38
	trophinin. [swissprot;acc:q12816]	TRO	Rooted	Subtracted	137.446	16.623	120.823
	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	PPP2R2D	Ranked		187.458	56.22	243.678
67	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	GBE1	Rooted		63.8686	16.6032	47.2654
	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	ARRB2	Measured	Divided	6475.5	1.59177	10307.5
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	ATG4B	Squared	Subtracted	144876	63739.5	81136.5
	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	GNAT2	Ranked	Divided	267.14	1.25805	336.075
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	MAGEA8	Squared		219048	1.68808	129762
	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	MYO15A	Rooted		63.8686	1.35128	47.2654
	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	RAF1	Measured	Subtracted	17756.5	3749.2	14007.3
	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]	PPP2R2B	Ranked		187.458	56.219	243.677
68	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	ARRB1	Measured	Divided	6475.5	1.59177	10307.5
	cyclin g2. [swissprot;acc:q16589]	CCNG2		Subtracted	17738.6	3742.9	13995.7
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	GABARAP	Squared		139741	61286.4	78454.6
	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	PYGB	Rooted		63.8686	16.6032	47.2654
	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	PYGM		Divided		1.35128
	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	GNAZ	Ranked		267.139	1.25805	336.075
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	MAGEC1	Squared		219048	1.68808	129762
	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]	PPP2R2C	Ranked	Subtracted	187.462	56.211	243.673
69	cyclin g1 (cyclin g). [swissprot;acc:p51959]	CCNG1	Measured		17738.5	3742.9	13995.6
	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	PYGL	Rooted		63.8686	16.6032	47.2654
	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	GNAT1	Ranked	Divided	267.14	1.25805	336.075
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	MAGEA4	Squared		219048	1.68808	129762
	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]	NDUFA12	Ranked	Subtracted	284.753	55.819	228.934
	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	NEUROD2	Rooted	Divided	27.9136	1.33581	37.2872
	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	PCF11	Squared	Subtracted	178263	59624	118639
	spermatogenesis associated 6. [refseq;acc:nm_019073]	SPATA6	Measured	Divided	6475.5	1.59177	10307.5
70	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	AMPD2
	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	CHD3	Rooted		27.9136	1.33581	37.2872
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	no value	Squared	Subtracted	129597	56439.5	73157.5
	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]	GNAI2	Ranked	Divided	267.142	1.25804	336.074
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	no value	Squared		219048	1.68808	129762
	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	MYO15A	Rooted	Subtracted	63.8686	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]	PPP2R5E	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]	PPP2R1B	Ranked		188.688	54.054	242.742
71	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	ATG3	Squared		129597	56439.5	73157.5

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.