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

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 444 to 493 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Hugo	Network Comparison Type	description	Value Type	red	network_comparison	green
56	HOXA5	Subtracted	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	Squared	173408	69581	242989
	MAGEB6B		melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Rooted	137.446	16.623	120.823
	PBK	Divided	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]	Measured	1631.67	1.63302	2664.55
	PYGL	Subtracted	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	Ranked	185.678	59.569	245.247
	RRAGA		ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Measured	20911	3997.5	24908.5
57	no value		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Squared	173408	69581	242989
			melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Rooted	137.446	16.623	120.823
	GNG12	Divided	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	Ranked	266.856	1.25998	336.233
	KCND3		potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]	Rooted	41.6879	1.43973	28.9554
	KHDRBS3		kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	Measured	1631.67	1.63302	2664.55
	MAGEA11		melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Squared	219048	1.68808	129762
	MYO15A	Subtracted	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	Ranked	185.678	59.569	245.247
	RRAGC		ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Measured	20911	3997.5	24908.5
58	GNG4	Divided	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Ranked	266.863	1.25979	336.191
	HSD17B14	Subtracted	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Squared	173408	69581	242989
	KCND1	Divided	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	Rooted	41.6969	1.43933	28.9696
	KHDRBS1		kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]	Measured	1631.67	1.63302	2664.55
	MAGEA2B		melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Squared	219048	1.68808	129762
	MAGEA9	Subtracted	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	Rooted	137.446	16.623	120.823
	PYGM		glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	Ranked	185.678	59.569	245.247
	RRAGB		ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Measured	20911	3997.5	24908.5
59	no value	Divided	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Squared	219048	1.68808	129762
	ANLN	Subtracted	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]	Measured	20911	3997.5	24908.5
	GNG3	Divided	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	Ranked	266.863	1.25978	336.19
	KCND2	Subtracted	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]		269.278	58.431	327.709
	KHDRBS2	Divided	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	Measured	1631.67	1.63302	2664.55
	MAGEA8	Subtracted	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Rooted	137.446	16.623	120.823
	NDUFA12	Divided	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]		37.2205	1.40262	52.2064
	PPP1CC	Subtracted	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873]	Squared	199594	69573	130021
60	no value		ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Measured	16771.5	3882.4	12889.1
	CTH		cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	Ranked	269.254	58.401	327.655
	GBE1	Divided	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Measured	4489.19	1.6231	2765.82
	GNG8		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	Ranked	266.864	1.25976	336.184
	MAGEA6		melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Squared	219048	1.68808	129762
	MAGEC1	Subtracted	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Rooted	137.446	16.623	120.823
	PPP1R2		protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	Squared	192904	66737	126167
	SON	Divided	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	Rooted	35.6294	1.39806	49.8119
61	ARRB2	Subtracted	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Measured	6475.5	3832	10307.5
	GNG5	Divided	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	Ranked	266.864	1.25975	336.182
	KCND3	Subtracted	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]		269.248	58.394	327.642
	KCNIP1	Divided	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Rooted	43.4291	1.36932	31.7159
	MAGEA4	Subtracted	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]		137.446	16.623	120.823
	NDN	Divided	necdin. [swissprot;acc:q99608]	Squared	219048	1.68808	129762
	PPP1R2P9	Subtracted	type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210]		192779	66684	126095
	PYGB	Divided	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	Measured	4489.19	1.6231	2765.82
62	no value	Subtracted	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Rooted	137.446	16.623	120.823
	ARRB1		beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Measured	6475.5	3832	10307.5
	GNG10	Divided	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	Ranked	266.865	1.25974	336.181
	KCND1	Subtracted	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]		269.23	58.371	327.601
	KCNIP4	Divided	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	Rooted	43.4519	1.36847	31.7522

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.