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

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Showing element 358 to 407 of 66312 in total

Filtered  : 1

Rank	description	Network Comparison Type	Hugo	Value Type	Interaction Map	red	green	network_comparison
23	glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335]	Subtracted	GNPDA2	Ranked	Low confidence	247.202	282.937	35.735
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	Divided	GNG3	Rooted	High confidence	40.3358	24.2919	1.66046
	implantation-associated protein. [refseq;acc:nm_032121]		no value	Ranked	Low confidence	198	163	1.21472
		Subtracted		Rooted		57.2538	71.1231	13.8693
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]			Measured	High confidence	23693.7	18263	5430.7
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]		MAGEA8	Squared		219048	129762	89286
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]		MFAP4	Ranked		322	253	69
	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]		MAP1LC3A	Rooted		153.578	133.176	20.402
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Divided	MAP1LC3B	Squared	Low confidence	78998	57169.1	1.38183
	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]		NEUROD2		High confidence	143.692	457.521	3.18404
	vasodilator-stimulated phosphoprotein (vasp). [swissprot;acc:p50552]	Subtracted	VASP		Low confidence	97360.9	72915.2	24445.7
24	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Divided	no value	Measured		5720.25	4577.5	1.24965
	bcl2-related ovarian killer. [refseq;acc:nm_032515]		BOK	Rooted		50.6099	61.2591	1.21042
	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Subtracted	CDK6	Measured		2399.5	543.5	1856
	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	Divided	CHD3	Squared	High confidence	143.692	457.521	3.18404
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	Subtracted	ATF3	Rooted	Low confidence	63.2736	76.7316	13.458
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]		ATG4B		High confidence	153.548	133.153	20.395
	ena/vasodilator stimulated phosphoprotein-like protein (ena/vasp-like protein). [swissprot;acc:q9ui08]		no value	Squared	Low confidence	97360.9	72915.2	24445.7
	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]		GNPDA1	Ranked		247.202	282.937	35.735
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	Divided	GNG8	Rooted	High confidence	40.336	24.2941	1.66032
	histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773]		HINT1	Ranked	Low confidence	188.298	228.509	1.21355
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Subtracted	MAGEA11	Measured	High confidence	23693.7	18263	5430.7
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]		MAGEC1	Squared		219048	129762	89286
	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	Divided	MAP1LC3A		Low confidence	78977.2	57161.1	1.38166
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]		PANK1	Ranked	High confidence	58	44	1.31818
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]		PRKRAP1	Measured		950.561	2108.52	2.21818
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Subtracted	PPP1R14D	Ranked		322	253	69
25	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	Divided	CYP27B1		Low confidence	286.396	238.476	1.20094
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Subtracted	ATG4A	Squared		80340.8	57685.7	22655.1
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Divided	ATG4B			77316.3	56522.1	1.3679
	doc-1 related protein (doc-1r). [swissprot;acc:o75956]		CDK2AP2		High confidence	143.692	457.521	3.18404
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Subtracted	FCN2	Ranked		322	253	69
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	Divided	GNG5	Rooted		40.3361	24.295	1.66026
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]		no value	Measured		1833.01	892.67	2.0534
	histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773]		HINT1		Low confidence	5847.46	4691.96	1.24627
				Rooted		67.7094	56.875	1.19049
	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Subtracted	LAMP2	Measured		2399.5	543.5	1856
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]		MAGEA4	Squared	High confidence	219048	129762	89286
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]		MAGEA2B	Measured		23693.7	18263	5430.7
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]		MYO5B	Rooted		146.94	167.046	20.106
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Divided	PANK2	Ranked		58	44	1.31818
	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]	Subtracted	PIGF		Low confidence	198	163	35
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]		UFC1	Rooted		53.5555	66.8994	13.3439
26	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]		CYP27B1			39.2301	52.5277	13.2976
	cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318]	Divided	CYP27A1	Ranked		286.347	238.454	1.20085
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]		GNG10	Rooted	High confidence	40.3362	24.2954	1.66024
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]		GNG12	Measured		1833.01	892.67	2.0534
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Subtracted	no value			23693.7	18263	5430.7
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]			Squared		219048	129762	89286
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]		MAP1LC3B		Low confidence	78998	57169.1	21828.9

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.