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 401 to 450 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
26	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	Squared	Divided	0	44.3683	0.344399	128.828
		Rooted			13.7805	3.80565	3.62106
	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	Ranked			12128.3	7533.33	1.60995
	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Measured			153	662	4.3268
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Rooted	Subtracted		40.0375	29.9666	10.0709
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]		Divided	1	40.3362	24.2954	1.66024
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	Measured			1833.01	892.67	2.0534
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]		Subtracted		23693.7	18263	5430.7
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Squared			219048	129762	89286
	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	Ranked		0	11284	17173.8	5889.8
	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Rooted		1	146.94	167.046	20.106
	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Squared	Divided		143.692	457.521	3.18404
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Ranked			58	44	1.31818
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]		Subtracted		322	253	69
	regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]	Squared		0	21273.2	12858.5	8414.7
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Measured			2965.5	2063	902.5
27	60s ribosomal protein l37a. [swissprot;acc:p12751]	Ranked			12941.7	18499.2	5557.5
		Rooted			13.7805	3.80565	9.97485
	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	Measured			14357.1	13463.1	894
	dystrophin. [swissprot;acc:p11532]	Rooted	Divided		17.8026	5.12693	3.47237
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Measured		1	1834.33	895.134	2.04922
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Rooted			40.3364	24.2968	1.66015
	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	Ranked	Subtracted		267.136	336.077	68.941
	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	Squared		0	151156	159204	8048
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]			1	219048	129762	89286
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Measured			23693.7	18263	5430.7
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Ranked	Divided		58	44	1.31818
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Rooted	Subtracted		146.94	167.046	20.106
	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	Squared	Divided		143.692	457.521	3.18404
	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	Measured		0	570	139	4.10072
	ptd016 protein. [refseq;acc:nm_016125]	Ranked			18050	11234	1.60673
	syntaxin 10 (syn10). [swissprot;acc:o60499]	Squared			4.29982	0.109658	39.2112
28	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	Ranked	Subtracted		12941.7	18499.2	5557.5
		Rooted			13.7805	3.80565	9.97485
	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Measured	Divided		570	139	4.10072
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	Ranked		1	201.949	153.671	1.31416
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Rooted	Subtracted		149.165	129.699	19.466
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]		Divided		40.3372	24.3043	1.65967
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	Measured			1834.36	895.194	2.04912
	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	Ranked	Subtracted		267.136	336.077	68.941
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Squared			219048	129762	89286
	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]			0	151156	159204	8048
	necdin. [swissprot;acc:q99608]	Measured		1	23693.7	18263	5430.7
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Squared	Divided		143.692	457.521	3.18404
	p28 ing5. [refseq;acc:nm_032329]	Ranked		0	12124.8	7562.05	1.60337
	ptd016 protein. [refseq;acc:nm_016125]	Squared			0.213018	5.90864	27.7377
	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6]	Measured	Subtracted		5418.2	4543.75	874.45
	syntaxin 10 (syn10). [swissprot;acc:o60499]	Rooted	Divided		9.62443	3.64637	2.63946
29	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Ranked	Subtracted		13730.5	8257	5473.5
	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Squared	Divided	1	143.692	457.521	3.18404

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.