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 13 to 62 of 3228 in total

Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	red	green	network_comparison
13	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	398.5	1281.5	3.21581
14	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]
15	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	2671	871	3.06659
16	protein x 0004. [refseq;acc:nm_016301]
17	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	460	1365	2.96739
18	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	677.5	1865.5	2.75351
19	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]
20	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]
21	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]
22	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]
23	gbp protein isoform a. [refseq;acc:nm_017870]	699.76	1894.39	2.7072
24	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	950.561	2108.52	2.21818
25	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	1833.01	892.67	2.0534
26	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]
27	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	1834.33	895.134	2.04922
28	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	1834.36	895.194	2.04912
29	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	1834.52	895.507	2.04858
30	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	1834.59	895.633	2.04837
31	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	1834.63	895.697	2.04827
32	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	1834.73	895.893	2.04793
33	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	1835.3	896.972	2.04611
34	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	1836.71	907.546	2.02382
35	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]		907.564	2.02378
36	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	1836.76	907.741	2.02344
37	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]		907.763	2.02339
38	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]		907.774	2.02337
39	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]	1836.8	907.903	2.02312
40	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]	1836.81	907.978	2.02297
41	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]
42	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775]	1857.32	958.237	1.93827
43	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]	1881.02	1027.36	1.83093
44	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]	1931.34	1057.39	1.82652
45	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]	1926.69	1056.02	1.82448
46	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	779.167	1390.33	1.78438
47	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]
48	doc-1 related protein (doc-1r). [swissprot;acc:o75956]
49	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]
50	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]
51	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]
52	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]
53	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]
54	deltex 2. [refseq;acc:nm_020892]	1618.84	2651.88	1.63814
55	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	1629.21	2662.12	1.63399
56	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]	1631.67	2664.55	1.63302
57	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]
58	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]
59	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]
60	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	4489.19	2765.82	1.6231
61	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]
62	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]

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.