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 5108 to 5157 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
320	coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621]	Squared	Subtracted	1	49280.5	42272.7	7007.8
	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]		Divided	0	5127.13	5964.46	1.16331
	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]		Subtracted		220.837	280.438	59.601
	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	Ranked	Divided	1	241.892	265.96	1.0995
	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099]	Squared			87971.9	69563.1	1.26463
	glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378]	Measured	Subtracted	0	996.883	1070.03	73.147
	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	Ranked		1	88.2482	110.265	22.0168
	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	Rooted	Divided	0	28.7027	26.9929	1.06334
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Measured		1	20911	24908.5	1.19117
	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718]		Subtracted		10263.8	11318.6	1054.8
	syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]		Divided	0	142.802	156.3	1.09452
	ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986]	Rooted	Subtracted		9.72761	8.25872	1.46889
	zinc finger protein 277. [swissprot;acc:q9nrm2]	Ranked			6279.56	5569.42	710.14
321	3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	Measured			2925.57	2853.65	71.92
	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]	Ranked	Divided		11634.4	10989.9	1.05864
	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]	Squared			5671.94	6590.82	1.162
	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Ranked		1	241.892	265.959	1.09949
	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959]	Squared	Subtracted	0	145.887	91.0551	54.8319
	dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513]	Measured	Divided		628.072	686.693	1.09333
	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	Rooted	Subtracted		41.1548	39.6879	1.4669
	fibulin-1 precursor. [swissprot;acc:p23142]	Squared		1	44407.1	51387.4	6980.3
	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]	Rooted			77.58	70.0181	7.5619
	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361]	Squared	Divided		33526	42390.2	1.2644
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	Ranked	Subtracted	0	10280.5	9574.98	705.52
	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Measured	Divided	1	20911	24908.5	1.19117
	signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473]		Subtracted		11797.1	10750.2	1046.9
	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538]	Rooted	Divided	0	42.9302	40.4104	1.06236
	trophinin. [swissprot;acc:q12816]	Ranked	Subtracted	1	88.2482	110.265	22.0168
	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	Rooted	Divided		55.9231	62.0565	1.10968
322	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	Measured		0	1621.1	1771.04	1.09249
	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]			1	20911	24908.5	1.19117
	carboxypeptidase b precursor. [refseq;acc:nm_020361]	Squared	Subtracted		25326.4	18354.1	6972.3
	casein kinase i alpha s-like. [refseq;acc:nm_145203]		Divided	0	7795.92	9052.52	1.16119
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Ranked		1	86.7483	78.8995	1.09948
	estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061]			0	11634.4	10989.9	1.05864
	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]	Squared	Subtracted		81.4343	135.97	54.5357
	neurocalcin delta. [swissprot;acc:p29554]	Measured			702.055	773.218	71.163
	nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531]	Squared	Divided	1	33522.8	42384.8	1.26436
	peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753]	Rooted	Subtracted	0	38.6064	40.0697	1.4633
	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]			1	77.5797	70.0179	7.5618
	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498]	Measured			9304.83	10347.3	1042.47
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	Ranked		0	10287.1	9583.27	703.83
	repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]	Rooted	Divided		46.9819	44.2892	1.0608
	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]			1	60.594	67.2244	1.10942
	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	Ranked	Subtracted		231.969	210.064	21.905
323	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]				242.238	264.11	21.872
	40s ribosomal protein s26. [swissprot;acc:p02383]	Measured		0	150.741	81.2233	69.5177
	60s ribosomal protein l23a. [swissprot;acc:p29316]	Ranked	Divided	1	241.884	265.945	1.09947
	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]	Rooted			50.3803	45.4193	1.10923
	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	Squared		0	5936.62	5112.71	1.16115

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.