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

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Showing element 1 to 50 of 19268 in total

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

red	Rank	Interaction Map	green	network_comparison	description
0.00001	501	High confidence	0.00001	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	500	High confidence	394		huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]
	840	Low confidence
772	433	High confidence	754	1.02387	trinucleotide repeat containing 15. [refseq;acc:nm_015575]
775	209		696	1.11351	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]
816	473		825	1.01103	cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098]
930	432		953	1.02473	fibrillin 3. [refseq;acc:nm_032447]
1091	307		1021	1.06856	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]
1251	243		1373	1.09752	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]
1256	622	Low confidence	1294	1.03025	caspr5 protein isoform 1. [refseq;acc:nm_130773]
	623				contactin associated protein-like 3 precursor (cell recognition molecule caspr3). [swissprot;acc:q9bz76]
1543	466	High confidence	1521	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
2584	450		2772	1.07276	hepatocellularcarcinoma-associated antigen hca557a. [refseq;acc:nm_015433]
2671.33	832		2668.83	1.00094	vps10 domain-containing receptor sorcs1 precursor (hsorcs). [swissprot;acc:q8wy21]
2939	448	High confidence	2876	1.02191	protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284]
	674	Low confidence
3032	602		3141	1.03595	erythropoietin 4 immediate early response; uncharacterized hypothalamus protein ht010. [refseq;acc:nm_018471]
3190	12		1933	1.65028	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]
3208.8	19		4871.6	1.5182	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]
	35	High confidence
3284	52		4554.5	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]
3464	262		3778	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]
3474	76		2695	1.28905	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]
3609	119		4302.5	1.19216	mesoderm induction early response 1. [refseq;acc:nm_020948]
3710	811	Low confidence	3724	1.00377	cervical cancer 1 protooncogene protein p40; regulator of tp53. [refseq;acc:nm_015416]
3845	40	High confidence	5699	1.48218	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
3859	21	Low confidence	2582	1.49458	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]
	37	High confidence
4119	72		5397	1.31027	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]
	73				phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669]
4222.84	157	Low confidence	4817.62	1.14085	zinc finger protein 75. [swissprot;acc:p51815]
4223.15	158		4817.95	1.14084	putative zinc finger protein (fragment). [sptrembl;acc:q8n692]
	159				zinc finger y-chromosomal protein. [swissprot;acc:p08048]
4224.28	160		4819.15	1.14082	zinc finger-like protein (fragment). [sptrembl;acc:q9uia8]
4224.79	161		4819.7	1.14081	ttf-i interacting peptide 20 (fragment). [sptrembl;acc:o00455]
4225.51	162		4820.46	1.1408	zinc finger protein 77 (znfpt1) (fragment). [swissprot;acc:q15935]
4234.54	163		4830.06	1.14063	zinc finger protein 32 (zinc finger protein kox30) (fragment). [swissprot;acc:p17041]
4238.74	164		4834.52	1.14056	zinc finger protein 95 homolog (zfp-95). [swissprot;acc:q9y2l8]
4239.56	165		4835.4	1.14054	zinc finger protein 80 (znfpt17). [swissprot;acc:p51504]
4240.02	166		4835.88	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.