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 2858 to 2907 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
179	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Measured	Divided	1	21591.5	27904.5	1.29238
	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5]	Rooted			50.272	43.4634	1.15665
	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	Ranked	Subtracted		227.357	254.15	26.793
	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]	Measured		0	304.664	483.809	179.145
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Squared		1	9924.76	25146.6	15221.8
	suppressor of actin 1. [refseq;acc:nm_014016]		Divided	0	0.284967	0.426714	1.49742
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Rooted			32.6268	28.4118	1.14835
180	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	Squared	Subtracted	1	9924.76	25146.6	15221.8
	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596]	Measured			10872.4	12447	1574.6
	dc11 protein. [refseq;acc:nm_020186]		Divided	0	556	681	1.22482
	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	Rooted		1	50.2801	43.4779	1.15645
	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	Squared	Subtracted	0	3680.39	3222.57	457.82
	keratin associated protein 1.5. [refseq;acc:nm_031957]	Rooted			23.8722	20.9331	2.9391
	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]			1	88.4361	77.5112	10.9249
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Measured	Divided		21591.5	27904.5	1.29238
	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]	Squared			25326.2	18354.1	1.37987
	pp3111 protein. [refseq;acc:nm_022156]	Ranked	Subtracted		227.357	254.15	26.793
	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]			0	7690.02	8991.19	1301.17
	purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]	Rooted	Divided		45.844	39.9449	1.14768
	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513]	Ranked			8407.67	9516.92	1.13193
	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]	Squared			38799.5	25982	1.49332
	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	Ranked		1	256.228	298.438	1.16474
	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]	Measured	Subtracted	0	304.664	483.809	179.145
181	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]				1318.22	1495.66	177.44
	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	Ranked	Divided	1	229.818	267.265	1.16294
	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	Rooted	Subtracted		88.4266	77.5047	10.9219
	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]		Divided		57.4432	66.3307	1.15472
	enigma protein; lim domain protein. [refseq;acc:nm_005451]	Measured		0	187.25	153	1.22386
	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]			1	4068.56	5252.6	1.29102
	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	Squared			55630.4	76083.7	1.36766
	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	Ranked		0	14864.7	16820.7	1.13159
	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]	Squared	Subtracted		3680.31	3222.51	457.8
	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]	Rooted			23.8722	20.9331	2.9391
	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]	Squared	Divided		140.822	210.151	1.49232
	musashi 2 isoform a. [refseq;acc:nm_138962]	Measured	Subtracted	1	4241.57	5810.79	1569.22
	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]	Ranked		0	4119	5397	1278
	syntaxin 18. [swissprot;acc:q9p2w9]			1	227.357	254.15	26.793
	transcription factor iib. [refseq;acc:nm_013242]	Squared			64739.9	50300.6	14439.3
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Rooted	Divided	0	28.1043	32.1981	1.14566
182	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	Measured	Subtracted		1317.84	1495.22	177.38
	chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286]	Rooted		1	47.6504	36.9304	10.72
	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	Squared	Divided	0	323.856	482.631	1.49026
	deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316]			1	61733.5	45224.1	1.36506
	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]	Rooted		0	31.1565	35.6653	1.14471
	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	Ranked		1	277.546	240.461	1.15422
	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	Rooted	Subtracted	0	23.8722	20.9331	2.9391
	keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]	Squared			3680.04	3222.31	457.73
	musashi 1. [refseq;acc:nm_002442]	Measured		1	4241.57	5810.79	1569.22
	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669]	Ranked		0	4119	5397	1278
	putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544]		Divided		11573.8	10231.3	1.13121

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.