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

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Showing element 1 to 50 of 19268 in total

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

green	red	Rank	Interaction Map	network_comparison	description
0.00001	0.00001	501	High confidence	1	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
		502			brca1 associated protein. [refseq;acc:nm_006768]
		837	Low confidence		gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
		838			gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
		839			cobw-like protein. [refseq;acc:nm_018491]
		841			gamma-glutamyltransferase. [sptrembl;acc:q14390]
		842			gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
		843			gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
394	394	500	High confidence		huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]
		840	Low confidence
696	775	209	High confidence	1.11351	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]
754	772	433		1.02387	trinucleotide repeat containing 15. [refseq;acc:nm_015575]
825	816	473		1.01103	cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098]
953	930	432		1.02473	fibrillin 3. [refseq;acc:nm_032447]
1021	1091	307		1.06856	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]
1294	1256	622	Low confidence	1.03025	caspr5 protein isoform 1. [refseq;acc:nm_130773]
		623			contactin associated protein-like 3 precursor (cell recognition molecule caspr3). [swissprot;acc:q9bz76]
1373	1251	243	High confidence	1.09752	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]
1521	1543	466		1.01446	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
		730	Low confidence
1933	3190	12		1.65028	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]
2582	3859	21		1.49458	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]
		37	High confidence
2668.83	2671.33	832	Low confidence	1.00094	vps10 domain-containing receptor sorcs1 precursor (hsorcs). [swissprot;acc:q8wy21]
2695	3474	76	High confidence	1.28905	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]
2772	2584	450	Low confidence	1.07276	hepatocellularcarcinoma-associated antigen hca557a. [refseq;acc:nm_015433]
2876	2939	448	High confidence	1.02191	protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284]
		674	Low confidence
3141	3032	602		1.03595	erythropoietin 4 immediate early response; uncharacterized hypothalamus protein ht010. [refseq;acc:nm_018471]
3724	3710	811		1.00377	cervical cancer 1 protooncogene protein p40; regulator of tp53. [refseq;acc:nm_015416]
3778	3464	262	High confidence	1.09065	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538]
4302.5	3609	119		1.19216	mesoderm induction early response 1. [refseq;acc:nm_020948]
4546.87	5677.96	86		1.24876	high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]
4547.43	5677.89	87		1.24859	dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]
4547.66	5677.86	88		1.24852	high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]
4549.85	5677.58	89		1.24786	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]
4550.87	5677.45	90		1.24755	high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]
4554.5	3284	52		1.38688	ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]
		53			ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966]
4817.62	4222.84	157	Low confidence	1.14085	zinc finger protein 75. [swissprot;acc:p51815]
4817.95	4223.15	158		1.14084	putative zinc finger protein (fragment). [sptrembl;acc:q8n692]
		159			zinc finger y-chromosomal protein. [swissprot;acc:p08048]
4819.15	4224.28	160		1.14082	zinc finger-like protein (fragment). [sptrembl;acc:q9uia8]
4819.7	4224.79	161		1.14081	ttf-i interacting peptide 20 (fragment). [sptrembl;acc:o00455]
4820.46	4225.51	162		1.1408	zinc finger protein 77 (znfpt1) (fragment). [swissprot;acc:q15935]
4830.06	4234.54	163		1.14063	zinc finger protein 32 (zinc finger protein kox30) (fragment). [swissprot;acc:p17041]
4834.52	4238.74	164		1.14056	zinc finger protein 95 homolog (zfp-95). [swissprot;acc:q9y2l8]
4835.4	4239.56	165		1.14054	zinc finger protein 80 (znfpt17). [swissprot;acc:p51504]
4835.88	4240.02	166		1.14053	zinc finger protein 187. [refseq;acc:nm_152736]
		167			zinc finger protein 302 (znf135-like) (znf140-like). [swissprot;acc:q9nr11]

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.