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

Results: HTML CSV LaTeX

Showing element 436 to 485 of 33156 in total

Network Comparison Type  : Divided
Filtered  : 1

Rank	Hugo	Value Type	description	Interaction Map	network_comparison	red	green
55	HOXA5	Squared	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	Low confidence	1.30449	122475	159767
	KCND2	Rooted	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	High confidence	1.44038	41.6734	28.9323
	MAGEE2	Squared	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]		1.68808	219048	129762
	PRKRAP1	Ranked	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]		1.26134	320.927	254.434
	SEPT10	Measured	septin 10 isoform 1. [refseq;acc:nm_144710]	Low confidence	1.13694	13081.2	14872.6
56	no value		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		1.13635	15464.1	17572.7
		Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	High confidence	1.25998	266.856	336.233
		Squared	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Low confidence	1.30449	122475	159767
			melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	High confidence	1.68808	219048	129762
	CTH	Rooted	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]		1.43986	41.6851	28.9509
	GSTO2		ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]	Low confidence	1.12389	62.7951	70.575
	PBK	Measured	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]	High confidence	1.63302	1631.67	2664.55
	T	Ranked	brachyury protein (t protein). [swissprot;acc:o15178]	Low confidence	1.11022	224.922	202.592
57	FOS		proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]		1.10985	202.802	182.73
	GNG12		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	High confidence	1.25998	266.856	336.233
	GSTO1	Rooted	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]	Low confidence	1.1207	63.0631	70.6746
	HOXB4	Measured	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]		1.13635	15464.1	17572.7
	HSD17B14	Squared	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]		1.30449	122475	159767
	KCND3	Rooted	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]	High confidence	1.43973	41.6879	28.9554
	KHDRBS3	Measured	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]		1.63302	1631.67	2664.55
	MAGEA11	Squared	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]		1.68808	219048	129762
58	no value	Ranked	jun dimerization protein. [refseq;acc:nm_130469]	Low confidence	1.10985	202.802	182.73
	GNG4		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	High confidence	1.25979	266.863	336.191
	HOXC5	Measured	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	Low confidence	1.13635	15464.1	17572.7
	KCND1	Rooted	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	High confidence	1.43933	41.6969	28.9696
	KHDRBS1	Measured	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]		1.63302	1631.67	2664.55
	MAGEA2B	Squared	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]		1.68808	219048	129762
	NDUFA12	Rooted	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]	Low confidence	1.11915	59.0909	66.1317
	PSCD1	Squared	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		1.29584	93450	72115.4
59	no value	Measured	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		1.13635	15464.1	17572.7
		Squared	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	High confidence	1.68808	219048	129762
			mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	Low confidence	1.29425	92930	71802.1
		Rooted	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]		1.11788	75.6323	67.6572
	GNG3	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	High confidence	1.25978	266.863	336.19
	KHDRBS2	Measured	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]		1.63302	1631.67	2664.55
	NDUFA12	Ranked	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]	Low confidence	1.10875	233.134	210.267
		Rooted		High confidence	1.40262	37.2205	52.2064
60	no value		cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238]	Low confidence	1.11478	59.2532	66.0541
	FOSL2	Ranked	fos-related antigen 2. [swissprot;acc:p15408]		1.10839	202.793	182.961
	GBE1	Measured	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	High confidence	1.6231	4489.19	2765.82
	GNG8	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]		1.25976	266.864	336.184
	HOXD4	Measured	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	Low confidence	1.13635	15464.1	17572.7
	MAGEA6	Squared	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	High confidence	1.68808	219048	129762
	PSCD2		cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Low confidence	1.29425	92930.5	71802.4
	SON	Rooted	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]	High confidence	1.39806	35.6294	49.8119
61	FOSB	Ranked	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Low confidence	1.10831	202.792	182.974
	GNG5		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	High confidence	1.25975	266.864	336.182
	HOXB5	Measured	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]	Low confidence	1.13635	15464.1	17572.7
	KCNIP1	Rooted	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	High confidence	1.36932	43.4291	31.7159
	NDN	Squared	necdin. [swissprot;acc:q99608]		1.68808	219048	129762

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.