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 1 to 50 of 502 in total

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

Rank	description	red	green	network_comparison
1	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	364	0.00001	36400000
2	cab2. [refseq;acc:nm_033419]	0.00001	174	17400000
3	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]		109	10900000
4	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		89	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	sedlin. [swissprot;acc:o14582]		43	4300000
8	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
9	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	85	6410	75.4118
10	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]
11	serpin b12. [swissprot;acc:q96p63]	199.549	5.56738	35.8425
12	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	199.249	5.71669	34.8539
13	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	1363	47	29
14	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	130.512	6.50325	20.0687
15	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]	10	156	15.6
16	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	1	15	15
17	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	859	58	14.8103
18	60s ribosomal protein l37a. [swissprot;acc:p12751]	305.45	26.1599	11.6763
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	ero1-like. [refseq;acc:nm_014584]	82	0.00001	8200000
21	syntaxin 10 (syn10). [swissprot;acc:o60499]	118.878	17.6611	6.73106
22	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	60	0.00001	6000000
23	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]	0.00001	59	5900000
24	ptd016 protein. [refseq;acc:nm_016125]	30	158	5.26667
25	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	148	773	5.22297
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]	153	662	4.3268
27	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	570	139	4.10072
28	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]
29	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	111.278	434.911	3.90833
30	dystrophin. [swissprot;acc:p11532]	427.217	111.739	3.82335
31	dok-like protein. [refseq;acc:nm_024872]	35	0.00001	3500000
32	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	598	184	3.25
33	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	12.6208	39.8063	3.15402
34	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	143	47	3.04255
35	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	459.5	1377	2.99674
36	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	157	56	2.80357
37	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	334.401	934.348	2.79409
38	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	320.012	120.429	2.65727
39	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	482.426	192.295	2.50878
40	nanos (fragment). [sptrembl;acc:q8wy41]	377	151	2.49669
41	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]	266	645	2.42481
42	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]	205.439	86.9525	2.36266
43	elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897]	263.66	587.988	2.2301
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]	45.4292	98.5074	2.16837
45	tigger transposable element derived 6. [refseq;acc:nm_030953]	202.374	438.605	2.1673
46	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	202.163	438.035	2.16674
47	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	202.156	438.016	2.16672
48	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	870.482	403.196	2.15895
49	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	72	151	2.09722
50	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	44	21	2.09524

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.