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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Filtered	Gene	Value Type	Network Comparison Type	Rank	description	Interaction Map	network_comparison	green	red

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Showing element 51 to 100 of 77072 in total

Filtered  : 0
Value Type  : Measured
Network Comparison Type  : Divided

Rank	description	Interaction Map	network_comparison	green	red
26	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	High confidence	4.3268	662	153
	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	Low confidence	3.04255	47	143
27	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]		2.97183	35.5	105.5
	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	High confidence	4.10072	139	570
28	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Low confidence	2.97183	35.5	105.5
29	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	High confidence	3.90833	434.911	111.278
30	dystrophin. [swissprot;acc:p11532]		3.82335	111.739	427.217
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Low confidence	2.97183	35.5	105.5
31	dok-like protein. [refseq;acc:nm_024872]	High confidence	3500000	0.00001	35
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Low confidence	2.97183	35.5	105.5
32	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	High confidence	3.25	184	598
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Low confidence	2.97183	35.5	105.5
33	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	High confidence	3.15402	39.8063	12.6208
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Low confidence	2.97183	35.5	105.5
34	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	High confidence	3.04255	47	143
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Low confidence	2.97183	35.5	105.5
35	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	High confidence	2.99674	1377	459.5
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Low confidence	2.97183	35.5	105.5
36	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	High confidence	2.80357	56	157
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	Low confidence	2.97183	35.5	105.5
37	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	High confidence	2.79409	934.348	334.401
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Low confidence	2.97183	35.5	105.5
38	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	High confidence	2.65727	120.429	320.012
39	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Low confidence	2.97183	35.5	105.5
	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	High confidence	2.50878	192.295	482.426
40	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Low confidence	2.97183	35.5	105.5
	nanos (fragment). [sptrembl;acc:q8wy41]	High confidence	2.49669	151	377
41	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Low confidence	2.97183	35.5	105.5
	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]	High confidence	2.42481	645	266
42	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Low confidence	2.97183	35.5	105.5
	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]	High confidence	2.36266	86.9525	205.439
43	elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897]		2.2301	587.988	263.66
	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]	Low confidence	2.97183	35.5	105.5
44	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]	High confidence	2.16837	98.5074	45.4292
	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Low confidence	28600000	0.00001	286
45	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]
	tigger transposable element derived 6. [refseq;acc:nm_030953]	High confidence	2.1673	438.605	202.374
46	ephrin type-b receptor 4 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor htk). [swissprot;acc:p54760]	Low confidence	2.79167	67	24
	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	High confidence	2.16674	438.035	202.163
47	tenascin-x precursor (tn-x) (hexabrachion-like). [swissprot;acc:p22105]	Low confidence	2.50526	776.89	310.103
	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	High confidence	2.16672	438.016	202.156
48	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]		2.15895	403.196	870.482
	pnas-129. [sptrembl;acc:q9bxv8]	Low confidence	2.42708	151.073	366.666
49	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]		2.42481	645	266
	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	High confidence	2.09722	151	72
50	latrophilin 2; lectomedin-1; latrophilin homolog 2 (cow). [refseq;acc:nm_012302]	Low confidence	2.36036	111	262
	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	High confidence	2.09524	21	44

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.