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 75 to 124 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
38	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]	Subtracted	266.933	333.281	66.348
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Divided	322	253	1.27273
39	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]	Subtracted	268.565	334.483	65.918
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Divided	322	253	1.27273
40	deltex 2. [refseq;acc:nm_020892]	Subtracted	333.144	267.393	65.751
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Divided	322	253	1.27273
41	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Subtracted	332.925	267.274	65.651
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Divided	322	253	1.27273
42	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]		204.641	160.957	1.2714
	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	Subtracted	332.874	267.246	65.628
43	jun dimerization protein. [refseq;acc:nm_130469]	Divided	204.641	160.957	1.2714
	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	Subtracted	332.874	267.246	65.628
44	fos-related antigen 2. [swissprot;acc:p15408]	Divided	204.641	161.046	1.2707
	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]	Subtracted	332.874	267.246	65.628
45	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Divided	204.641	161.051	1.27066
46	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]		204.642	161.068	1.27053
	neuralized-like. [refseq;acc:nm_004210]	Subtracted	332.326	266.948	65.378
47	gbp protein isoform a. [refseq;acc:nm_017870]	Divided	325.586	256.492	1.26938
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Subtracted	350	290	60
48	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Divided	65.4586	83.0461	1.26868
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Subtracted	350	290	60
49	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Divided	133	105	1.26667
	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Subtracted	350	290	60
50	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Divided	133	105	1.26667
	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Subtracted	350	290	60
51	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Divided	133	105	1.26667
52	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Subtracted	350	290	60
53	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181]		318.982	259.004	59.978
	transcription factor jun-b. [swissprot;acc:p17275]	Divided	201.144	158.868	1.26611
54	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Subtracted	185.678	245.247	59.569
	transcription factor jun-d. [swissprot;acc:p17535]	Divided	200.941	158.941	1.26425
55	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	Subtracted	185.678	245.247	59.569
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Divided	320.927	254.434	1.26134
56	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	Subtracted	185.678	245.247	59.569
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Divided	266.856	336.233	1.25998
57	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]
	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	Subtracted	185.678	245.247	59.569
58	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Divided	266.863	336.191	1.25979
59	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]			336.19	1.25978
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Subtracted	269.278	327.709	58.431
60	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]		269.254	327.655	58.401
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	Divided	266.864	336.184	1.25976
61	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]			336.182	1.25975
	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]	Subtracted	269.248	327.642	58.394
62	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	Divided	266.865	336.181	1.25974
	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	Subtracted	269.23	327.601	58.371

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.