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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Gene	Rank	description	Value Type	Network Comparison Type	Interaction Map	Filtered	green	red	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	green	red	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	0.344399	44.3683	128.828
		Rooted			3.80565	13.7805	3.62106
	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	Ranked			7533.33	12128.3	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			662	153	4.3268
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Rooted	Subtracted		29.9666	40.0375	10.0709
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]		Divided	1	24.2954	40.3362	1.66024
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	Measured			892.67	1833.01	2.0534
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]		Subtracted		18263	23693.7	5430.7
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Squared			129762	219048	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	17173.8	11284	5889.8
	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Rooted		1	167.046	146.94	20.106
	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Squared	Divided		457.521	143.692	3.18404
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Ranked			44	58	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		253	322	69
	regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]	Squared		0	12858.5	21273.2	8414.7
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Measured			2063	2965.5	902.5
27	60s ribosomal protein l37a. [swissprot;acc:p12751]	Ranked			18499.2	12941.7	5557.5
		Rooted			3.80565	13.7805	9.97485
	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	Measured			13463.1	14357.1	894
	dystrophin. [swissprot;acc:p11532]	Rooted	Divided		5.12693	17.8026	3.47237
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Measured		1	895.134	1834.33	2.04922
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Rooted			24.2968	40.3364	1.66015
	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	Ranked	Subtracted		336.077	267.136	68.941
	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	Squared		0	159204	151156	8048
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]			1	129762	219048	89286
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Measured			18263	23693.7	5430.7
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Ranked	Divided		44	58	1.31818
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Rooted	Subtracted		167.046	146.94	20.106
	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	Squared	Divided		457.521	143.692	3.18404
	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	Measured		0	139	570	4.10072
	ptd016 protein. [refseq;acc:nm_016125]	Ranked			11234	18050	1.60673
	syntaxin 10 (syn10). [swissprot;acc:o60499]	Squared			0.109658	4.29982	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		18499.2	12941.7	5557.5
		Rooted			3.80565	13.7805	9.97485
	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Measured	Divided		139	570	4.10072
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	Ranked		1	153.671	201.949	1.31416
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Rooted	Subtracted		129.699	149.165	19.466
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]		Divided		24.3043	40.3372	1.65967
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	Measured			895.194	1834.36	2.04912
	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	Ranked	Subtracted		336.077	267.136	68.941
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Squared			129762	219048	89286
	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]			0	159204	151156	8048
	necdin. [swissprot;acc:q99608]	Measured		1	18263	23693.7	5430.7
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Squared	Divided		457.521	143.692	3.18404
	p28 ing5. [refseq;acc:nm_032329]	Ranked		0	7562.05	12124.8	1.60337
	ptd016 protein. [refseq;acc:nm_016125]	Squared			5.90864	0.213018	27.7377
	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6]	Measured	Subtracted		4543.75	5418.2	874.45
	syntaxin 10 (syn10). [swissprot;acc:o60499]	Rooted	Divided		3.64637	9.62443	2.63946
29	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Ranked	Subtracted		8257	13730.5	5473.5
	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Squared	Divided	1	457.521	143.692	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.