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	Value Type	description	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 180 to 229 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	Value Type	description	Filtered	red	green	network_comparison
23	Ranked	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	0	15520.4	9285.44	1.67148
	Squared	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		174.646	0.796213	219.346
		neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	1	143.692	457.521	3.18404
	Rooted	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]		40.3358	24.2919	1.66046
		protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	0	1	3.87298	3.87298
24	Measured	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	1	950.561	2108.52	2.21818
		ptd016 protein. [refseq;acc:nm_016125]	0	30	158	5.26667
	Ranked	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		13730.5	8257	1.66289
		pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	1	58	44	1.31818
	Squared	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]		143.692	457.521	3.18404
		cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	0	4.16226	0.02001	208.009
	Rooted	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	1	40.336	24.2941	1.66032
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	0	29.3087	7.61577	3.84842
25	Measured	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	1	1833.01	892.67	2.0534
		potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	0	148	773	5.22297
	Ranked	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]		13730.5	8257	1.66289
		pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	1	58	44	1.31818
	Squared	60s ribosomal protein l37a. [swissprot;acc:p12751]	0	44.3683	0.344399	128.828
		doc-1 related protein (doc-1r). [swissprot;acc:o75956]	1	143.692	457.521	3.18404
	Rooted	60s ribosomal protein l37a. [swissprot;acc:p12751]	0	13.7805	3.80565	3.62106
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	1	40.3361	24.295	1.66026
26	Measured	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	0	153	662	4.3268
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	1	1833.01	892.67	2.0534
	Ranked	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	0	12128.3	7533.33	1.60995
		pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	1	58	44	1.31818
	Squared	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]	0	44.3683	0.344399	128.828
		neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	1	143.692	457.521	3.18404
	Rooted	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]	0	13.7805	3.80565	3.62106
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	1	40.3362	24.2954	1.66024
27	Measured	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]		1834.33	895.134	2.04922
		phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	0	570	139	4.10072
	Ranked	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	1	58	44	1.31818
		ptd016 protein. [refseq;acc:nm_016125]	0	18050	11234	1.60673
	Squared	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	1	143.692	457.521	3.18404
		syntaxin 10 (syn10). [swissprot;acc:o60499]	0	4.29982	0.109658	39.2112
	Rooted	dystrophin. [swissprot;acc:p11532]		17.8026	5.12693	3.47237
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	1	40.3364	24.2968	1.66015
28	Measured	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	0	570	139	4.10072
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	1	1834.36	895.194	2.04912
	Ranked	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]		201.949	153.671	1.31416
		p28 ing5. [refseq;acc:nm_032329]	0	12124.8	7562.05	1.60337
	Squared	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	1	143.692	457.521	3.18404
		ptd016 protein. [refseq;acc:nm_016125]	0	0.213018	5.90864	27.7377
	Rooted	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	1	40.3372	24.3043	1.65967
		syntaxin 10 (syn10). [swissprot;acc:o60499]	0	9.62443	3.64637	2.63946
29	Measured	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	1	1834.52	895.507	2.04858
		potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	0	111.278	434.911	3.90833
	Ranked	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]		7395	11625	1.57201
		uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	1	187.458	243.678	1.29991
	Squared	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]		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.