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 1323 to 1372 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
83	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	Measured	Divided	1	4932.27	7033.29	1.42597
	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172]	Squared			117718	70505.9	1.66962
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]	Rooted			63.6507	48.7127	1.30666
	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	Ranked		0	18359.8	14447.8	1.27077
	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]		Subtracted		18079	15652	2427
	uridine kinase-like 1. [swissprot;acc:q9nwz5]	Squared	Divided		269.31	688.46	2.55638
84	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]			1	117515	70412.3	1.66896
	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]			0	33.0303	83.901	2.54012
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	Rooted	Subtracted	1	40.3358	24.2919	16.0439
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Ranked	Divided		88.2482	110.265	1.24949
	homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]		Subtracted		252.296	201.995	50.301
	jun dimerization protein. [refseq;acc:nm_130469]	Measured	Divided		4932.27	7033.29	1.42597
	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]	Rooted			46.7419	60.9337	1.30362
	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	Measured		0	973.698	1601.52	1.64478
	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	Rooted	Subtracted		11.2068	16.7658	5.559
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Squared		1	103496	146848	43352
	regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]	Rooted	Divided	0	33.5215	25.0836	1.33639
	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]	Measured	Subtracted		3336.48	2957.12	379.36
	syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]	Ranked	Divided		12460.6	15781	1.26647
	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]	Squared	Subtracted		5317.39	3738.08	1579.31
	transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854]	Ranked			12946.3	10519.7	2426.6
	type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210]	Measured		1	21632.5	18090	3542.5
85	autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]	Squared	Divided		67438.6	40697	1.65709
	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]			0	181.122	444.663	2.45505
	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]	Rooted		1	46.7419	60.9337	1.30362
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]		Subtracted	0	18.1049	12.6095	5.4954
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]		Divided		40.0375	29.9666	1.33607
	fos-related antigen 2. [swissprot;acc:p15408]	Measured		1	4941.95	7037.11	1.42395
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	Rooted	Subtracted		40.336	24.2941	16.0419
	heat shock factor binding protein 1. [swissprot;acc:o75506]	Squared		0	3647.42	2072.05	1575.37
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Ranked	Divided	1	88.2482	110.265	1.24949
	nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]	Measured	Subtracted	0	266	645	379
	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]		Divided		679.449	1106.88	1.62908
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Squared	Subtracted	1	103496	146848	43352
	ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050]	Measured			21370.8	17896.5	3474.3
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Ranked			296.677	247.559	49.118
	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]		Divided	0	9688.47	12104.2	1.24934
			Subtracted				2415.73
86	60s ribosomal protein l21. [swissprot;acc:p46778]	Squared	Divided		146.619	359.589	2.45254
	alpha crystallin a chain. [swissprot;acc:p02489]	Measured			55.3059	89.2447	1.61366
		Ranked	Subtracted		16372.4	13972.2	2400.2
	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	Squared			3480.56	5039.04	1558.48
	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	Ranked		1	335	286	49
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	Rooted			40.3361	24.295	16.0411
	high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]	Ranked	Divided	0	5677.96	4546.87	1.24876
	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]	Rooted			9.13761	12.1722	1.3321
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Ranked		1	88.2482	110.265	1.24949
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Measured			4942.49	7037.32	1.42384
	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Squared	Subtracted		103496	146848	43352
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Rooted		0	40.4536	35.073	5.3806

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.