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 2363 to 2412 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
148	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Squared	Divided	1	103496	146848	1.41888
	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858]		Subtracted		70011	49783	20228
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Ranked	Divided		296.677	247.559	1.19841
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Squared	Subtracted	0	978.105	1746.18	768.075
	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6]	Ranked	Divided		6755.71	7863.63	1.164
	symplekin. [swissprot;acc:q92797]	Measured	Subtracted	1	15213.4	13418.1	1795.3
149	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	Squared		0	2783.53	3517.26	733.73
	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]		Divided	1	103496	146848	1.41888
	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Ranked			142	170	1.19718
	block 23. [sptrembl;acc:q8nhw5]			0	11469.3	13334.8	1.16265
	cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]	Measured			293.178	379.474	1.29435
	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Rooted		1	42.0684	50.4323	1.19882
	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]			0	8.52047	10.0173	1.17567
	metaxin 1. [swissprot;acc:q13505]	Squared	Subtracted	1	60401.6	79875.7	19474.1
	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	Ranked		0	13942.8	15586.4	1643.6
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Measured	Divided	1	11068	8508.5	1.30082
	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]		Subtracted	0	323.79	544.991	221.201
	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	Rooted		1	41.6969	28.9696	12.7273
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Squared	Divided	0	8.27669	4.90793	1.68639
	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	Ranked	Subtracted	1	226.582	198.444	28.138
	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Rooted		0	133.419	129.687	3.732
	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648]	Measured		1	11736.6	13531.9	1795.3
150	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]	Rooted			42.2825	54.9687	12.6862
	dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]	Squared		0	3966.2	3268.89	697.31
	dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513]	Ranked			7495.26	9130.38	1635.12
	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084]	Squared		1	57913.5	76336.3	18422.8
	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]		Divided	0	274.947	163.071	1.68606
	metaxin 1. [swissprot;acc:q13505]	Measured			933.395	723.368	1.29035
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Ranked		1	55	46	1.19565
	pnas-18. [sptrembl;acc:q9bzu3]	Measured	Subtracted	0	2256.05	2035.28	220.77
	pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989]	Squared	Divided	1	121200	85473.4	1.41799
	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	Ranked	Subtracted		226.582	198.444	28.138
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Measured	Divided		11068	8508.5	1.30082
	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361]	Rooted		0	26.8649	22.8761	1.17437
	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]			1	63.5827	53.0856	1.19774
	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	Measured	Subtracted		4172.91	5954.48	1781.57
	zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]	Ranked	Divided	0	8730	7516	1.16152
		Rooted	Subtracted		19.6214	23.3024	3.681
151	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]		Divided	1	38.8223	46.4975	1.1977
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	Squared		0	25050	42114.6	1.68122
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]			1	250303	354894	1.41786
	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099]		Subtracted		87971.9	69563.1	18408.8
	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	Rooted			50.3065	62.9788	12.6723
	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]			0	22.775	19.1245	3.6505
	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Ranked	Divided	1	55	46	1.19565
	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466]		Subtracted	0	7234.6	8858.94	1624.34
	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	Squared			396.995	1088.19	691.195
	pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989]	Measured		1	14830.5	13050.3	1780.2
	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	Ranked			226.582	198.444	28.138
	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	Measured	Divided		4578.09	5939.91	1.29746

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.