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 714 to 763 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
45	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	Ranked	Subtracted	1	332.874	267.246	65.628
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Squared			110342	184298	73956
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Ranked	Divided		204.641	161.051	1.27066
	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Measured	Subtracted		27642.5	22440.4	5202.1
	tigger transposable element derived 6. [refseq;acc:nm_030953]		Divided	0	202.374	438.605	2.1673
	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	Squared			14.8569	83.2781	5.60535
	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]		Subtracted		25574.2	20063.8	5510.4
46	60s ribosomal protein l37a. [swissprot;acc:p12751]	Ranked	Divided		12941.7	18499.2	1.42943
	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	Squared		1	129597	73157.5	1.77148
	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	Measured	Subtracted		24896.4	20431.7	4464.7
	deltex 2. [refseq;acc:nm_020892]	Rooted	Divided		27.634	43.9629	1.5909
	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	Squared	Subtracted	0	30195	24837.5	5357.5
	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	Ranked	Divided	1	204.642	161.068	1.27053
	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]		Subtracted	0	5210.5	9264.5	4054
	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	Rooted	Divided		12.53	7.48331	1.67439
	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]		Subtracted		25.1701	33.2721	8.102
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]			1	137.446	120.823	16.623
	neuralized-like. [refseq;acc:nm_004210]	Ranked			332.326	266.948	65.378
	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	Measured	Divided		779.167	1390.33	1.78438
	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	Squared	Subtracted		210445	136779	73666
	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	Measured		0	3023.85	2436.4	587.45
	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	Squared	Divided		14.8562	83.274	5.60534
	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	Measured			202.163	438.035	2.16674
47	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			12941.7	18499.2	1.42943
	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	Rooted			21.3967	34.6716	1.62042
	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	Measured		1	779.167	1390.33	1.78438
	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Rooted			27.7078	44.017	1.58861
	exocyst complex component sec5. [swissprot;acc:q96kp1]	Squared	Subtracted		210335	136716	73619
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]		Divided	0	975.125	178.265	5.47009
	gbp protein isoform a. [refseq;acc:nm_017870]	Ranked		1	325.586	256.492	1.26938
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Rooted	Subtracted		137.446	120.823	16.623
	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	Squared		0	36059.4	30745.3	5314.1
	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]	Rooted			24.6374	32.6803	8.0429
	testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562]	Ranked			15352	11346.5	4005.5
	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	Measured	Divided		202.156	438.016	2.16672
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Ranked	Subtracted	1	350	290	60
	trs85 homolog. [swissprot;acc:q9y2l5]	Measured			24896.4	20431.7	4464.7
	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258]			0	3645.5	3118.3	527.2
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Squared	Divided	1	98517.9	56927.2	1.73059
48	60s acidic ribosomal protein p1. [swissprot;acc:p05386]		Subtracted	0	49458.1	54614.9	5156.8
	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Measured	Divided		870.482	403.196	2.15895
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]		Subtracted		999.28	481.725	517.555
	doc-1 related protein (doc-1r). [swissprot;acc:o75956]		Divided	1	779.167	1390.33	1.78438
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Ranked			65.4586	83.0461	1.26868
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Squared		0	960.518	176.164	5.45241
	importin 9. [refseq;acc:nm_018085]	Rooted	Subtracted		21.8651	29.828	7.9629
	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	Squared	Divided	1	6300.2	10703.5	1.69891
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Rooted	Subtracted		137.446	120.823	16.623
	nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]	Ranked	Divided	0	9830	6909	1.42278
	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	Squared	Subtracted	1	210199	136638	73561

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.