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 4158 to 4207 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
260	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	Rooted	Subtracted	1	56.7592	65.9889	9.2297
	surfeit locus protein 5. [swissprot;acc:q15528]	Ranked			242.14	265.696	23.556
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Measured	Divided	0	1949.36	2202	1.1296
261	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	Ranked			12448.9	11393.9	1.09259
		Rooted	Subtracted		21.1334	23.34	2.2066
	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]		Divided		22.315	24.6198	1.10328
	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	Squared			135280	170628	1.2613
	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Measured			1295.81	1463.55	1.12945
	carboxypeptidase a5. [refseq;acc:nm_080385]	Squared	Subtracted	1	53174	44377.4	8796.6
	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	Rooted			52.7582	61.9123	9.1541
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]	Ranked	Divided		219.421	196.978	1.11394
	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]		Subtracted	0	13651	14572	921
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Squared			6.25494	141.944	135.689
	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]	Measured			205.439	86.9525	118.486
	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498]	Squared	Divided	1	48127.9	62245.6	1.29334
	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	Rooted			62.3337	70.0738	1.12417
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Measured			4247.36	5192.61	1.22255
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]		Subtracted		4571.89	5864.86	1292.97
	zinc finger protein 291. [swissprot;acc:q9by12]	Ranked			242.14	265.696	23.556
262	3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	Squared		0	18353.1	18218.3	134.8
	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]		Divided		2463.89	3102.4	1.25915
	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	Rooted			26.0693	28.761	1.10325
	adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123]	Measured			764.479	676.971	1.12926
	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	Ranked	Subtracted		9984	9067	917
	carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086]	Squared		1	53174	44377.4	8796.6
	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	Measured	Divided		24896.4	20431.7	1.21852
	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]		Subtracted	0	606.049	723.75	117.701
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]	Ranked	Divided	1	219.421	196.978	1.11394
	integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106]	Rooted	Subtracted	0	19.303	21.5023	2.1993
	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	Squared	Divided	1	26157.6	20236.2	1.29261
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Measured	Subtracted		4571.89	5864.86	1292.97
	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]	Ranked			242.14	265.696	23.556
	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	Rooted	Divided		59.4073	66.7002	1.12276
	rna-binding protein. [refseq;acc:nm_019027]		Subtracted		52.7642	61.9019	9.1377
	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]	Ranked	Divided	0	3464	3778	1.09065
263	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]	Squared		1	26157.6	20236.2	1.29261
	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	Rooted		0	4.79583	4.3589	1.10024
	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]		Subtracted	1	52.7642	61.9019	9.1377
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Ranked	Divided	0	13573.3	14801.2	1.09046
	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	Measured	Subtracted		498.07	615.233	117.163
	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	Squared			2892.28	2758.62	133.66
	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]	Measured		1	4571.89	5864.86	1292.97
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]	Ranked	Divided		219.421	196.978	1.11394
	neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837]	Squared	Subtracted		53174	44377.4	8796.6
	paxillin. [swissprot;acc:p49023]	Rooted	Divided		59.4073	66.7002	1.12276
	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	Ranked	Subtracted	0	8786.74	7870.3	916.44
	protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530]			1	242.14	265.696	23.556
	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	Squared	Divided	0	2463.98	3102.52	1.25915
	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]	Measured			1843	1633	1.1286
	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	Rooted	Subtracted		137.437	139.628	2.191

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.