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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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

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Showing element 1375 to 1424 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
86	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Measured	Subtracted	0	1526.38	1150.51	375.87
	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116]	Squared	Divided	1	105500	64146.3	1.64468
87	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]	Rooted			42.2825	54.9687	1.30003
	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]	Squared	Subtracted		103496	146848	43352
	chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286]	Ranked			249.663	298.263	48.6
	dead-box protein. [refseq;acc:nm_018665]	Rooted		0	16.237	10.8929	5.3441
	dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]	Ranked	Divided		5677.89	4547.43	1.24859
	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	Rooted			17.7787	23.6792	1.33189
	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	Measured		1	4944.3	7038.04	1.42347
	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388]		Subtracted	0	1283.48	1649.37	365.89
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	Rooted		1	40.3362	24.2954	16.0408
	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13]	Squared	Divided		105482	64136.9	1.64464
	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]	Ranked	Subtracted	0	16411.9	14027.1	2384.8
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]		Divided	1	88.2482	110.265	1.24949
	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	Measured	Subtracted		20287.2	17083.8	3203.4
	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	Squared	Divided	0	0.668702	1.63441	2.44415
	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]	Measured			304.664	483.809	1.58801
	similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]	Squared	Subtracted		14693.6	16237.1	1543.5
88	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Rooted		1	40.3364	24.2968	16.0396
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Ranked	Divided		88.2482	110.265	1.24949
	high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]			0	5677.86	4547.66	1.24852
	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	Rooted			3.4819	4.6274	1.32899
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Measured	Subtracted		364	0	364
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	Ranked			12787.8	10454.7	2333.1
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Measured	Divided	1	2411.93	1695.45	1.42259
	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	Rooted			37.3005	48.4141	1.29795
	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]	Squared			105482	64137.2	1.64463
	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795]	Ranked	Subtracted		249.663	298.263	48.6
	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	Squared		0	7073.9	8609.96	1536.06
	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]	Measured	Divided		304.664	483.809	1.58801
	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116]		Subtracted	1	16074	12888.4	3185.6
	transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854]	Squared	Divided	0	13.9318	32.9409	2.36444
	tubby protein homolog. [swissprot;acc:p50607]	Rooted	Subtracted		39.7788	45.0452	5.2664
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Squared		1	98517.9	56927.2	41590.7
89	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]	Ranked		0	12049	14370.7	2321.7
	block 23. [sptrembl;acc:q8nhw5]	Squared			14555.7	16084.7	1529
	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	Measured	Divided	1	2414.22	1698.12	1.4217
	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	Rooted		0	39.9124	52.9528	1.32673
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]		Subtracted	1	40.3372	24.3043	16.0329
	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	Measured		0	4088	4451	363
	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	Squared	Divided		21.5282	9.12314	2.35974
	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13]	Measured	Subtracted	1	16071.6	12886.8	3184.8
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Ranked	Divided		88.2482	110.265	1.24949
	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]			0	5677.58	4549.85	1.24786
	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]	Rooted	Subtracted		14.1508	8.89106	5.25974
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Ranked		1	249.663	298.263	48.6
	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991]	Rooted	Divided		37.3005	48.4141	1.29795
	suppressor of actin 1. [refseq;acc:nm_014016]	Measured		0	23.6076	37.4843	1.58781
	transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112]	Squared		1	105473	64132.3	1.64462
	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116]		Subtracted		105500	64146.3	41353.7

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
- 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.