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

Results: HTML CSV LaTeX

Showing element 330 to 379 of 66312 in total

Filtered  : 1

Rank	description	Hugo	Value Type	Network Comparison Type	Interaction Map	red	green	network_comparison
21	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	no value	Squared	Subtracted	High confidence	219048	129762	89286
	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	MYO15A	Ranked	Divided		185.678	245.247	1.32082
	n33 protein. [swissprot;acc:q13454]	TUSC3	Rooted		Low confidence	57.2538	71.1231	1.24224
	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]	PIGF	Ranked			198	163	1.21472
			Rooted	Subtracted		57.2538	71.1231	13.8693
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	UBAC1	Squared	Divided		189688	134787	1.40732
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	TOB1	Ranked	Subtracted		296.837	258.33	38.507
22	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	ATG4A	Squared	Divided		80340.8	57685.7	1.39273
	cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973]	CYP24A1	Measured			3126.88	3997.02	1.27828
	dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985]	MAP2K4	Ranked	Subtracted		210.241	246.125	35.884
	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	PYGM		Divided	High confidence	185.678	245.247	1.32082
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	GNG4	Rooted			40.3357	24.2915	1.66049
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	MAGEE2	Measured	Subtracted		23693.7	18263	5430.7
	implantation-associated protein. [refseq;acc:nm_032121]	no value	Rooted	Divided	Low confidence	57.2538	71.1231	1.24224
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	LAMP1	Measured	Subtracted		2399.5	543.5	1856
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	MAGEA9	Squared		High confidence	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	Rooted			153.578	133.176	20.402
	n33 protein. [swissprot;acc:q13454]	TUSC3	Ranked	Divided	Low confidence	198	163	1.21472
			Rooted	Subtracted		57.2538	71.1231	13.8693
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	PPP1R14A	Ranked		High confidence	322	253	69
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	no value	Measured	Divided		677.5	1865.5	2.75351
			Squared			108.641	823.69	7.58176
	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	HSD17B14		Subtracted	Low confidence	122475	159767	37292
23	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	MRPS17	Ranked	Divided	High confidence	58	44	1.31818
	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	CPD	Measured		Low confidence	40899	32028.5	1.27696
	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	CDK4		Subtracted		2399.5	543.5	1856
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	ATF3	Rooted	Divided		63.2736	76.7316	1.2127
	gbp protein isoform a. [refseq;acc:nm_017870]	TMEM132A	Measured		High confidence	699.76	1894.39	2.7072
	glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335]	GNPDA2	Ranked	Subtracted	Low confidence	247.202	282.937	35.735
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	GNG3	Rooted	Divided	High confidence	40.3358	24.2919	1.66046
	implantation-associated protein. [refseq;acc:nm_032121]	no value	Ranked		Low confidence	198	163	1.21472
			Rooted	Subtracted		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]	MAP1LC3B	Squared	Divided	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]	VASP		Subtracted	Low confidence	97360.9	72915.2	24445.7
24	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	no value	Measured	Divided		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]	CDK6	Measured	Subtracted		2399.5	543.5	1856
	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	CHD3	Squared	Divided	High confidence	143.692	457.521	3.18404
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	ATF3	Rooted	Subtracted	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]	GNG8	Rooted	Divided	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]	MAGEA11	Measured	Subtracted	High confidence	23693.7	18263	5430.7

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.