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

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Showing element 1 to 50 of 14920 in total

Value Type  : Measured
Filtered  : 0
Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	green	description	network_comparison	red
1	0.00001	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	36400000	364
2	174	cab2. [refseq;acc:nm_033419]	17400000	0.00001
3	109	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	10900000
4	89	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	8900000
5		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
6		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
7	43	sedlin. [swissprot;acc:o14582]	4300000
8		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
9	6410	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	75.4118	85
10		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]
11	5.56738	serpin b12. [swissprot;acc:q96p63]	35.8425	199.549
12	5.71669	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	34.8539	199.249
13	47	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	29	1363
14	6.50325	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	20.0687	130.512
15	156	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]	15.6	10
16	15	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	15	1
17	58	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14.8103	859
18	26.1599	60s ribosomal protein l37a. [swissprot;acc:p12751]	11.6763	305.45
19		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]
20	0.00001	ero1-like. [refseq;acc:nm_014584]	8200000	82
21	17.6611	syntaxin 10 (syn10). [swissprot;acc:o60499]	6.73106	118.878
22	0.00001	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	6000000	60
23	59	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	5900000	0.00001
24	158	ptd016 protein. [refseq;acc:nm_016125]	5.26667	30
25	773	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	5.22297	148
26	662	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	4.3268	153
27	139	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	4.10072	570
28		beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]
29	434.911	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	3.90833	111.278
30	111.739	dystrophin. [swissprot;acc:p11532]	3.82335	427.217
31	0.00001	dok-like protein. [refseq;acc:nm_024872]	3500000	35
32	184	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	3.25	598
33	39.8063	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	3.15402	12.6208
34	47	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	3.04255	143
35	1377	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	2.99674	459.5
36	56	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	2.80357	157
37	934.348	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	2.79409	334.401
38	120.429	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	2.65727	320.012
39	192.295	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	2.50878	482.426
40	151	nanos (fragment). [sptrembl;acc:q8wy41]	2.49669	377
41	645	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	266
42	86.9525	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]	2.36266	205.439
43	587.988	elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897]	2.2301	263.66
44	98.5074	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]	2.16837	45.4292
45	438.605	tigger transposable element derived 6. [refseq;acc:nm_030953]	2.1673	202.374
46	438.035	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	2.16674	202.163
47	438.016	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	2.16672	202.156
48	403.196	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	2.15895	870.482
49	151	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	2.09722	72
50	21	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	2.09524	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.