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 1510 to 1559 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
95	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	Ranked	Divided	1	88.2482	110.265	1.24949
	metaxin 1. [swissprot;acc:q13505]	Rooted		0	14.7289	11.2174	1.31304
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Measured			154	0.00001	15400000
	pp3111 protein. [refseq;acc:nm_022156]	Ranked			6185	7603	1.22926
	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Squared		1	256169	162517	1.57626
	rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736]	Ranked	Subtracted		249.663	298.263	48.6
	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795]	Rooted	Divided		47.6504	36.9304	1.29028
	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	Measured			2397.19	3343.62	1.39481
	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]	Squared		0	631.532	280.389	2.25234
	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625]		Subtracted	1	123324	86277.9	37046.1
	zinc finger protein 232. [swissprot;acc:q9uny5]	Ranked		0	11523.7	13686.9	2163.2
96	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Squared	Divided	1	7744.68	4959.41	1.56161
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	Ranked	Subtracted		201.949	153.671	48.278
	elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897]	Measured		0	263.66	587.988	324.328
	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	Squared	Divided		52.0821	116.513	2.2371
	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]	Rooted	Subtracted	1	40.28	24.37	15.91
	high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]	Squared		0	311980	313369	1389
	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	Ranked	Divided		8335.82	10228.3	1.22703
	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	Measured		1	4110.14	5694.99	1.3856
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Ranked			88.2482	110.265	1.24949
	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	Rooted	Subtracted	0	27.4843	22.4483	5.036
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]		Divided	1	47.6504	36.9304	1.29028
	septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599]	Measured	Subtracted		16177.9	19235.4	3057.5
		Squared			90226	126939	36713
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Measured	Divided	0	154	0.00001	15400000
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Rooted			65.4535	49.8523	1.31295
	zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028]	Ranked	Subtracted		11523	13685.4	2162.4
97	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]	Measured	Divided		728.65	476.619	1.52879
	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]			1	2820.51	3897.1	1.3817
		Ranked	Subtracted		271.752	225.68	46.072
	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]	Squared	Divided		227160	146079	1.55505
	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]		Subtracted		126408	89940.5	36467.5
	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]	Rooted			40.2797	24.3705	15.9092
	integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106]	Squared		0	6188.69	7568.12	1379.43
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Ranked	Divided	1	88.2482	110.265	1.24949
	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]			0	8335.82	10228.3	1.22703
	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Squared			10489.8	23426.5	2.23326
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Measured	Subtracted		111.278	434.911	323.633
	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	Rooted			22.2259	17.2182	5.0077
	regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081]		Divided	1	47.6504	36.9304	1.29028
	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]			0	13.2903	17.4395	1.3122
	septin 10 isoform 1. [refseq;acc:nm_144710]	Measured	Subtracted	1	16067.4	19094.4	3027
	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58]	Ranked		0	11522.8	13684.9	2162.1
98	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	Rooted			83.9673	88.8829	4.9156
	brain protein 44. [swissprot;acc:o95563]	Measured		1	15999.1	19007.1	3008
	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]	Rooted			40.2797	24.3705	15.9092
	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	Measured		0	39165	39485	320
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Ranked	Divided	1	88.2482	110.265	1.24949
	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]	Squared	Subtracted	0	310884	312261	1377
	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466]	Ranked	Divided		7234.6	8858.94	1.22452

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.