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	Filtered	red	Interaction Map	network_comparison	green

Results: HTML CSV LaTeX

Showing element 401 to 450 of 38536 in total

Network Comparison Type  : Divided

Rank	Value Type	description	Filtered	red	Interaction Map	network_comparison	green
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	High confidence	4.3268	662
		glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]		143	Low confidence	3.04255	47
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	1	1833.01	High confidence	2.0534	892.67
		sperm associated antigen 7. [refseq;acc:nm_004890]		23318	Low confidence	1.20939	19280.8
	Ranked	cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318]		286.347		1.20085	238.454
		dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	0	12128.3	High confidence	1.60995	7533.33
		folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]		9282.29	Low confidence	1.42223	6526.57
		pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	1	58	High confidence	1.31818	44
	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		128.828	0.344399
		melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]		3.41692	Low confidence	9.62112	0.355148
		neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	1	143.692	High confidence	3.18404	457.521
		vasodilator-stimulated phosphoprotein (vasp). [swissprot;acc:p50552]		97360.9	Low confidence	1.33526	72915.2
	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	High confidence	3.62106	3.80565
		cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2]		12.4097	Low confidence	1.78921	22.2036
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	1	40.3362	High confidence	1.66024	24.2954
		son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]		51.3588	Low confidence	1.1826	60.737
27	Measured	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]		1834.33	High confidence	2.04922	895.134
		melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	0	105.5	Low confidence	2.97183	35.5
		phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]		570	High confidence	4.10072	139
		protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	1	3840.85	Low confidence	1.20152	4614.87
	Ranked	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]	0	13109		1.41246	18516
		cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973]	1	284.798		1.19792	237.743
		mitochondrial solute carrier protein. [refseq;acc:nm_145305]		58	High confidence	1.31818	44
		ptd016 protein. [refseq;acc:nm_016125]	0	18050		1.60673	11234
	Squared	ena/vasodilator stimulated phosphoprotein-like protein (ena/vasp-like protein). [swissprot;acc:q9ui08]	1	97360.9	Low confidence	1.33526	72915.2
		melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	0	3.41692		9.62112	0.355148
		neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	1	143.692	High confidence	3.18404	457.521
		syntaxin 10 (syn10). [swissprot;acc:o60499]	0	4.29982		39.2112	0.109658
	Rooted	dystrophin. [swissprot;acc:p11532]		17.8026		3.47237	5.12693
		glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335]	1	52.3425	Low confidence	1.1617	45.0567
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]		40.3364	High confidence	1.66015	24.2968
		pnas-129. [sptrembl;acc:q9bxv8]	0	16.4276	Low confidence	1.77673	9.246
28	Measured	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]		570	High confidence	4.10072	139
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	1	1834.36		2.04912	895.194
		melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	0	105.5	Low confidence	2.97183	35.5
		tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	1	3098.94		1.2003	3719.66
	Ranked	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]		142		1.19718	170
		cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]		201.949	High confidence	1.31416	153.671
		elongation of very long chain fatty acids protein 2. [swissprot;acc:q9nxb9]	0	16116.4	Low confidence	1.40082	11505
		p28 ing5. [refseq;acc:nm_032329]		12124.8	High confidence	1.60337	7562.05
	Squared	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	1	82347.8	Low confidence	1.33073	61881.5
		melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	0	3.41692		9.62112	0.355148
		neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	1	143.692	High confidence	3.18404	457.521
		ptd016 protein. [refseq;acc:nm_016125]	0	0.213018		27.7377	5.90864
	Rooted	cab2. [refseq;acc:nm_033419]		5.30308	Low confidence	1.74737	9.26646
		glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	1	52.3425		1.1617	45.0567
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]		40.3372	High confidence	1.65967	24.3043
		syntaxin 10 (syn10). [swissprot;acc:o60499]	0	9.62443		2.63946	3.64637
29	Measured	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	1	1834.52		2.04858	895.507
		melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	0	105.5	Low confidence	2.97183	35.5

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.