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

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Showing element 1 to 50 of 9634 in total

Value Type  : Ranked
Network Comparison Type  : Divided

Rank	Filtered	description	Interaction Map	red	green	network_comparison
1	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	High confidence	4294	15915	3.70633
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Low confidence	5865	14977	2.55362
	1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]		16	32	2
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	High confidence	10	24	2.4
2	0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Low confidence	8906	21883	2.45711
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	High confidence	5865	14977	2.55362
	1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Low confidence	223	330	1.47982
		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]	High confidence	15	28	1.86667
3	0	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Low confidence	9607	20617	2.14604
		nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	High confidence	4475.84	11083.9	2.47638
	1	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Low confidence	223	330	1.47982
		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	High confidence	15	28	1.86667
4	0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		8906	21883	2.45711
		neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]	Low confidence	9607	20617	2.14604
	1	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]		223	330	1.47982
		cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	High confidence	15	28	1.86667
5	0	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]		5510.5	11965.7	2.17144
		ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	Low confidence	10889.4	19873	1.82499
	1	cytohesin 4. [swissprot;acc:q9uia0]	High confidence	15	28	1.86667
		lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Low confidence	223	330	1.47982
6	0	trinucleotide repeat containing 15. [refseq;acc:nm_015575]		5575.71	9583.37	1.71877
		ubiquitin protein ligase. [refseq;acc:nm_130466]	High confidence	7523	15339.2	2.03897
	1	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		15	28	1.86667
		oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	Low confidence	318	240	1.325
7	0	cab2. [refseq;acc:nm_033419]	High confidence	21866	10950	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]	Low confidence	11543	6812	1.69451
	1	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	High confidence	215	322	1.49767
		oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Low confidence	318	240	1.325
8	0	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		22286	13216	1.68629
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	High confidence	11525	21888	1.89918
	1	hbs1-like. [refseq;acc:nm_006620]		215	322	1.49767
		oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]	Low confidence	318	240	1.325
9	0	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		22286	13216	1.68629
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	High confidence	11525	21888	1.89918
	1	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Low confidence	58	44	1.31818
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	High confidence	212	309	1.45755
10	0	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
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Low confidence	22286	13216	1.68629
	1	mitochondrial solute carrier protein. [refseq;acc:nm_145305]		58	44	1.31818
		protein x 0004. [refseq;acc:nm_016301]	High confidence	212	309	1.45755
11	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Low confidence	13730.5	8257	1.66289
		potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	High confidence	11627	6248	1.86092
	1	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	Low confidence	37.318	28.4944	1.30966
		rad50-interacting protein 1. [refseq;acc:nm_021930]	High confidence	337	232	1.45259
12	0	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	Low confidence	3190	1933	1.65028
		folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	High confidence	9429.18	5208.84	1.81023
	1	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]		337	232	1.45259
		vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]	Low confidence	37.3475	28.5242	1.30933
13	0	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	High confidence	5210.5	9264.5	1.77804
		sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796]	Low confidence	7435.56	12191.6	1.63963

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.