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 2080 to 2129 of 6456 in total

Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
1040	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]	Divided	5421.93	5926.08	1.09298
1041	dead-box protein. [refseq;acc:nm_018665]	Subtracted	5719.01	6248.6	529.59
	myb-related protein a (a-myb). [swissprot;acc:p10243]	Divided	5419.18	5922.84	1.09294
1042	histone h2b.c (h2b/c). [swissprot;acc:q99880]	Subtracted	3946.32	4475.47	529.15
	similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2]	Divided	5887.52	6434.32	1.09287
1043	15 kda selenoprotein precursor. [swissprot;acc:o60613]		6344.41	6933.36	1.09283
	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]	Subtracted	3946.32	4475.47	529.15
1044	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]
	mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517]	Divided	4757.46	5198.91	1.09279
1045	histone h2b. [refseq;acc:nm_175055]	Subtracted	3946.32	4475.47	529.15
	immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197]	Divided	5364.32	5862.09	1.09279
1046	histone h2b.s (h2b/s). [swissprot;acc:p57053]	Subtracted	3946.32	4475.47	529.15
	skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9]	Divided	4757.46	5198.91	1.09279
1047	histone h2b.d (h2b/d). [swissprot;acc:q99877]	Subtracted	3946.32	4475.47	529.15
	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]	Divided	4757.46	5198.91	1.09279
1048	histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]	Subtracted	3946.32	4475.47	529.15
	tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289]	Divided	4757.46	5198.91	1.09279
1049	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]
	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610]	Subtracted	3946.32	4475.47	529.15
1050	histone h2b.e (h2b/e). [swissprot;acc:q99879]
	neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1]	Divided	4757.46	5198.91	1.09279
1051	homeobox protein dlx-2. [swissprot;acc:q07687]
	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	Subtracted	5208.27	5737.17	528.9
1052	homeobox protein dlx-5. [swissprot;acc:p56178]	Divided	4757.46	5198.91	1.09279
	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031]	Subtracted	6278.76	6807.51	528.75
1053	fetal brain protein 239 (239fb). [swissprot;acc:q15777]	Divided	4757.46	5198.91	1.09279
	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	Subtracted	5166.04	5694.55	528.51
1054	heat shock factor binding protein 1. [swissprot;acc:o75506]		5915.42	6443.77	528.35
	homeobox protein dlx-3. [swissprot;acc:o60479]	Divided	4757.46	5198.91	1.09279
1055	activated p21cdc42hs kinase. [refseq;acc:nm_005781]
	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	Subtracted	5167.15	5695.44	528.29
1056	mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093]	Divided	4757.46	5198.91	1.09279
	xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736]	Subtracted	6413.32	6941.48	528.16
1057	mitochondrial translational release factor 1-like. [refseq;acc:nm_019041]		5168.01	5696.12	528.11
	tata element modulatory factor (tmf). [swissprot;acc:p82094]	Divided	5412.23	5913.4	1.0926
1058	protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706]	Subtracted	6275.86	6803.95	528.09
	scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680]	Divided	5412.23	5913.4	1.0926
1059	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886]	Subtracted	3853.64	4379.71	526.07
	tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814]	Divided	5719.01	6248.6	1.0926
1060	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	Subtracted	5791.05	6316.61	525.56
	putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305]	Divided	5719.01	6248.6	1.0926
1061	hskin17 protein. [refseq;acc:nm_012311]	Subtracted	5791.05	6316.61	525.56
	nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948]	Divided	5412.23	5913.4	1.0926
1062	ammecr1 protein. [refseq;acc:nm_015365]
	carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155]	Subtracted	5791.05	6316.61	525.56
1063	mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406]	Divided	5412.23	5913.4	1.0926
	polyadenylate-binding protein 4 (poly(a)-binding protein 4) (pabp 4) (inducible poly(a)-binding protein) (ipabp) (activated-platelet protein-1) (app-1). [swissprot;acc:q13310]	Subtracted	5791.05	6316.61	525.56
1064	dead-box protein. [refseq;acc:nm_018665]	Divided	5719.01	6248.6	1.0926
	polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940]	Subtracted	5791.05	6316.61	525.56
1065	dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887]		6350.81	6874.88	524.07

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.