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

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Showing element 1 to 50 of 9634 in total

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

Rank	description	green	Interaction Map	red	network_comparison
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	High confidence	4294	3.70633
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	Low confidence	5865	2.55362
2	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883		8906	2.45711
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	High confidence	5865	2.55362
3	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	20617	Low confidence	9607	2.14604
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	11083.9	High confidence	4475.84	2.47638
4	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883		8906	2.45711
	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]	20617	Low confidence	9607	2.14604
5	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	11965.7	High confidence	5510.5	2.17144
	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	19873	Low confidence	10889.4	1.82499
6	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	9583.37		5575.71	1.71877
	ubiquitin protein ligase. [refseq;acc:nm_130466]	15339.2	High confidence	7523	2.03897
7	cab2. [refseq;acc:nm_033419]	10950		21866	1.99689
	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	6812	Low confidence	11543	1.69451
8	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	13216		22286	1.68629
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	21888	High confidence	11525	1.89918
9	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	13216	Low confidence	22286	1.68629
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	21888	High confidence	11525	1.89918
10	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	14178.1		7509.39	1.88805
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	13216	Low confidence	22286	1.68629
11	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	8257		13730.5	1.66289
	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	6248	High confidence	11627	1.86092
12	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	1933	Low confidence	3190	1.65028
	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	5208.84	High confidence	9429.18	1.81023
13	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	9264.5		5210.5	1.77804
	sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796]	12191.6	Low confidence	7435.56	1.63963
14	dystrophin. [swissprot;acc:p11532]	18054.8	High confidence	10232.5	1.76446
	ptd016 protein. [refseq;acc:nm_016125]	11234	Low confidence	18050	1.60673
15	adenomatous polyposis coli like. [refseq;acc:nm_005883]	7597.61		12074.1	1.5892
	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]	11267	High confidence	19403	1.72211
16	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	11625	Low confidence	7395	1.57201
	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	20670.6	High confidence	12170.7	1.69839
17	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	6812		11543	1.69451
	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	5266.67	Low confidence	8082.33	1.53462
18	early hematopoietic zinc finger. [refseq;acc:nm_015461]	8903.28		5850.23	1.52187
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	13216	High confidence	22286	1.68629
19	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	4871.6	Low confidence	3208.8	1.5182
20	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]	14964		22422	1.4984
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	13216	High confidence	22286	1.68629
21	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	10621.4		6313.38	1.68236
	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	2582	Low confidence	3859	1.49458
22	cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2]	7867		11515	1.46371
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	12479	High confidence	20989	1.68195
23	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	9285.44		15520.4	1.67148
	serpin b12. [swissprot;acc:q96p63]	21138.6	Low confidence	14604.2	1.44743
24	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	8257	High confidence	13730.5	1.66289
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	21113.7	Low confidence	14592	1.44694
25	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	8257	High confidence	13730.5	1.66289
	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]	6909	Low confidence	9830	1.42278

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.