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

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Showing element 1 to 50 of 9634 in total

Value Type  : Ranked
Network Comparison Type  : Divided

Rank	Interaction Map	description	green	network_comparison	red	Filtered
1	High confidence	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	3.70633	4294	0
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	24	2.4	10	1
	Low confidence	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	32	2	16
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	2.55362	5865	0
2	High confidence	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	28	1.86667	15	1
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	2.55362	5865	0
	Low confidence	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	330	1.47982	223	1
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883	2.45711	8906	0
3	High confidence	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	28	1.86667	15	1
		nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	11083.9	2.47638	4475.84	0
	Low confidence	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	330	1.47982	223	1
		neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	20617	2.14604	9607	0
4	High confidence	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	28	1.86667	15	1
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883	2.45711	8906	0
	Low confidence	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	330	1.47982	223	1
		neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]	20617	2.14604	9607	0
5	High confidence	cytohesin 4. [swissprot;acc:q9uia0]	28	1.86667	15	1
		ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	11965.7	2.17144	5510.5	0
	Low confidence	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	330	1.47982	223	1
		ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	19873	1.82499	10889.4	0
6	High confidence	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	28	1.86667	15	1
		ubiquitin protein ligase. [refseq;acc:nm_130466]	15339.2	2.03897	7523	0
	Low confidence	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	240	1.325	318	1
		trinucleotide repeat containing 15. [refseq;acc:nm_015575]	9583.37	1.71877	5575.71	0
7	High confidence	cab2. [refseq;acc:nm_033419]	10950	1.99689	21866
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	322	1.49767	215	1
	Low confidence	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	1.69451	11543	0
		oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	240	1.325	318	1
8	High confidence	hbs1-like. [refseq;acc:nm_006620]	322	1.49767	215
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	21888	1.89918	11525	0
	Low confidence	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	13216	1.68629	22286
		oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]	240	1.325	318	1
9	High confidence	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	21888	1.89918	11525	0
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	309	1.45755	212	1
	Low confidence	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	44	1.31818	58
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	13216	1.68629	22286	0
10	High confidence	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	14178.1	1.88805	7509.39
		protein x 0004. [refseq;acc:nm_016301]	309	1.45755	212	1
	Low confidence	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	13216	1.68629	22286	0
		mitochondrial solute carrier protein. [refseq;acc:nm_145305]	44	1.31818	58	1
11	High confidence	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	6248	1.86092	11627	0
		rad50-interacting protein 1. [refseq;acc:nm_021930]	232	1.45259	337	1
	Low confidence	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	8257	1.66289	13730.5	0
		bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	28.4944	1.30966	37.318	1
12	High confidence	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	5208.84	1.81023	9429.18	0
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	232	1.45259	337	1
	Low confidence	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	1933	1.65028	3190	0
		vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]	28.5242	1.30933	37.3475	1
13	High confidence	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	9264.5	1.77804	5210.5	0
		protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	212.554	1.3585	288.754	1

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.