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 80 to 129 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
40	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	Subtracted	23693.7	18263	5430.7
41	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]	Divided	1836.81	907.978	2.02297
	trophinin. [swissprot;acc:q12816]	Subtracted	23693.7	18263	5430.7
42	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]		21785.2	16426.1	5359.1
	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775]	Divided	1857.32	958.237	1.93827
43	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	Subtracted	21785.2	16426.1	5359.1
	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]	Divided	1881.02	1027.36	1.83093
44	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Subtracted	28136.5	33457.6	5321.1
	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]	Divided	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
	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Subtracted	27642.5	22440.4	5202.1
46	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]		24896.4	20431.7	4464.7
	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	Divided	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]
	trs85 homolog. [swissprot;acc:q9y2l5]	Subtracted	24896.4	20431.7	4464.7
48	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	Divided	779.167	1390.33	1.78438
	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	Subtracted	24806.9	20369.9	4437
49	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Divided	779.167	1390.33	1.78438
50	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	Subtracted	24473.9	20127.8	4346.1
	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	Divided	779.167	1390.33	1.78438
51	fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917]	Subtracted	23640.2	19479.8	4160.4
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Divided	779.167	1390.33	1.78438
52	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]
	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	Subtracted	23422.4	19380.3	4042.1
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]	Divided	779.167	1390.33	1.78438
	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	Subtracted	23326.5	19296.4	4030.1
54	deltex 2. [refseq;acc:nm_020892]	Divided	1618.84	2651.88	1.63814
	exocyst complex component sec5. [swissprot;acc:q96kp1]	Subtracted	23316	19288.8	4027.2
55	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Divided	1629.21	2662.12	1.63399
	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	Subtracted	23303.1	19279.5	4023.6
56	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]		20911	24908.5	3997.5
	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]	Divided	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]
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Subtracted	20911	24908.5	3997.5
58	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]	Divided	1631.67	2664.55	1.63302
	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Subtracted	20911	24908.5	3997.5
59	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]
	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	Divided	1631.67	2664.55	1.63302
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
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Subtracted	16771.5	12889.1	3882.4
61	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]		6475.5	10307.5	3832
	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	Divided	4489.19	2765.82	1.6231
62	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Subtracted	6475.5	10307.5	3832
	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	Divided	4489.19	2765.82	1.6231
63	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Subtracted	6475.5	10307.5	3832
64	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	Divided	4489.19	2765.82	1.6231
65	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	Subtracted	22515.5	18702.6	3812.9

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.