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	Hugo	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  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 0

Rank	Hugo	description	red	green	network_comparison
1	ARFGAP3	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	4294	15915	3.70633
2	STARD3	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	5865	14977	2.55362
3	no value	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	4475.84	11083.9	2.47638
4		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	8906	21883	2.45711
5		ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	5510.5	11965.7	2.17144
6	UBE3B	ubiquitin protein ligase. [refseq;acc:nm_130466]	7523	15339.2	2.03897
7	PERLD1	cab2. [refseq;acc:nm_033419]	21866	10950	1.99689
8	no value	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	11525	21888	1.89918
9	TBL1Y	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
10	FBP2	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	7509.39	14178.1	1.88805
11	ATP9A	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	11627	6248	1.86092
12	FPGS	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	9429.18	5208.84	1.81023
13	no value	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	5210.5	9264.5	1.77804
14		dystrophin. [swissprot;acc:p11532]	10232.5	18054.8	1.76446
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]	19403	11267	1.72211
16	CCNH	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	12170.7	20670.6	1.69839
17	no value	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	11543	6812	1.69451
18		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	22286	13216	1.68629
19		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
20		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
21	ACRC	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	6313.38	10621.4	1.68236
22	PNPO	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	20989	12479	1.68195
23	HGS	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	15520.4	9285.44	1.67148
24	no value	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	13730.5	8257	1.66289
25		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]
26	DTNBP1	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	12128.3	7533.33	1.60995
27	no value	ptd016 protein. [refseq;acc:nm_016125]	18050	11234	1.60673
28	ING5	p28 ing5. [refseq;acc:nm_032329]	12124.8	7562.05	1.60337
29	PNMT	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	7395	11625	1.57201
30	no value	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]
31	LRRFIP1	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	8082.33	5266.67	1.53462
32	no value	importin 9. [refseq;acc:nm_018085]	13292.2	8691.76	1.52929
33		nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]
34	MAPRE2	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	11284	17173.8	1.52196
35	no value	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	3208.8	4871.6	1.5182
36	GNB1L	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]	22422	14964	1.4984
37	no value	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	3859	2582	1.49458
38	CDK8	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	7230	10771	1.48976
39	no value	ero1-like. [refseq;acc:nm_014584]	13853	20536	1.48242
40		filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	3845	5699	1.48218
41		60s ribosomal protein l21. [swissprot;acc:p46778]	9994.33	6758.83	1.47871
42	SLC25A6	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	8158	5530.5	1.47509
43	GSTT2B	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	12143.8	8356.02	1.4533
44	SERPINB12	serpin b12. [swissprot;acc:q96p63]	14604.2	21138.6	1.44743
45	no value	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	14592	21113.7	1.44694
46		60s ribosomal protein l37a. [swissprot;acc:p12751]	12941.7	18499.2	1.42943
47	CYP27B1	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]
48	NDUFA5	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]	9830	6909	1.42278
49	no value	brain protein 16. [refseq;acc:nm_016458]	6890.54	4854.99	1.41927
50	COMP	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	9249.73	13091.4	1.41533

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
- Hugo is the HGNC identifier if it exists
- 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.