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

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Showing element 1 to 50 of 19268 in total

Value Type  : Ranked
Filtered  : 0

Rank	Network Comparison Type	red	Interaction Map	green	description	network_comparison
1	Divided	4294	High confidence	15915	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	3.70633
		5865	Low confidence	14977	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	2.55362
	Subtracted	8906	High confidence	21883	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	12977
			Low confidence
2	Divided	5865	High confidence	14977	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	2.55362
		8906	Low confidence	21883	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	2.45711
	Subtracted	4294	High confidence	15915	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	11621
		9607	Low confidence	20617	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	11010
3	Divided	4475.84	High confidence	11083.9	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	2.47638
		9607	Low confidence	20617	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	2.14604
	Subtracted				neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]	11010
		21866	High confidence	10950	cab2. [refseq;acc:nm_033419]	10916
4	Divided	8906		21883	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	2.45711
		9607	Low confidence	20617	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]	2.14604
	Subtracted	5865		14977	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	9112
		11525	High confidence	21888	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	10363
5	Divided	5510.5		11965.7	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	2.17144
		10889.4	Low confidence	19873	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	1.82499
	Subtracted	11525	High confidence	21888	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	10363
		22286	Low confidence	13216	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	9070
6	Divided	5575.71		9583.37	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	1.71877
		7523	High confidence	15339.2	ubiquitin protein ligase. [refseq;acc:nm_130466]	2.03897
	Subtracted	5865		14977	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	9112
		22286	Low confidence	13216	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	9070
7	Divided	11543		6812	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	1.69451
		21866	High confidence	10950	cab2. [refseq;acc:nm_033419]	1.99689
	Subtracted	22286		13216	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	9070
			Low confidence		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
8	Divided	11525	High confidence	21888	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	1.89918
		22286	Low confidence	13216	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	1.68629
	Subtracted	10889.4		19873	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	8983.6
		22286	High confidence	13216	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	9070
9	Divided	11525		21888	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	1.89918
		22286	Low confidence	13216	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	1.68629
	Subtracted		High confidence		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	9070
		22422	Low confidence	14964	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]	7458
10	Divided	7509.39	High confidence	14178.1	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	1.88805
		22286	Low confidence	13216	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	1.68629
	Subtracted	18050		11234	ptd016 protein. [refseq;acc:nm_016125]	6816
		20989	High confidence	12479	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	8510
11	Divided	11627		6248	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	1.86092
		13730.5	Low confidence	8257	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	1.66289
	Subtracted	12170.7	High confidence	20670.6	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	8499.9
		14604.2	Low confidence	21138.6	serpin b12. [swissprot;acc:q96p63]	6534.4
12	Divided	3190		1933	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	1.65028
		9429.18	High confidence	5208.84	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	1.81023
	Subtracted	14592	Low confidence	21113.7	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	6521.7
		19403	High confidence	11267	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]	8136
13	Divided	5210.5		9264.5	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	1.77804
		7435.56	Low confidence	12191.6	sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796]	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.