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

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Showing element 1 to 50 of 77072 in total

Filtered  : 0
Value Type  : Measured

Rank	Network Comparison Type	description	Interaction Map	network_comparison	red	green
1	Divided	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	High confidence	36400000	364	0.00001
			Low confidence
	Subtracted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	High confidence	6325	85	6410
			Low confidence
2	Divided	cab2. [refseq;acc:nm_033419]	High confidence	17400000	0.00001	174
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Low confidence	8900000		89
	Subtracted	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	High confidence	6325	85	6410
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Low confidence	4196.8	23818.1	19621.3
3	Divided	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		8900000	0.00001	89
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	High confidence	10900000		109
	Subtracted	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		4196.8	23818.1	19621.3
		nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Low confidence	2393.82	5106.93	7500.75
4	Divided	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]		8900000	0.00001	89
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	High confidence
	Subtracted	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	Low confidence	2274	2082	4356
		small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	High confidence	3026	18704	21730
5	Divided	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		8900000	0.00001	89
		jumonji protein. [swissprot;acc:q92833]	Low confidence	1751660		17.5166
	Subtracted	histone h4. [swissprot;acc:p02304]	High confidence	2673.2	21773.1	24446.3
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Low confidence	2254.84	485.286	2740.13
6	Divided	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	High confidence	8900000	0.00001	89
		homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Low confidence	1300000	13	0.00001
	Subtracted	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	High confidence	2430.4	13174.7	15605.1
			Low confidence	1244.48	7592.37	8836.85
7	Divided	sedlin. [swissprot;acc:o14582]	High confidence	4300000	0.00001	43
		tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	Low confidence	231962	2.31962	0.00001
	Subtracted	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		1238.62	4660.09	5898.71
		zinc finger protein 277. [swissprot;acc:q9nrm2]	High confidence	2430.4	13174.7	15605.1
8	Divided	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Low confidence	75.4118	85	6410
		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	High confidence	4300000	0.00001	43
	Subtracted	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]		2393.82	5106.93	7500.75
		zinc finger protein 277. [swissprot;acc:q9nrm2]	Low confidence	1232.83	7537.89	8770.72
9	Divided	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	High confidence	75.4118	85	6410
		ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	Low confidence	36.1876	383.762	10.6048
	Subtracted	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	High confidence	2278	12478	14756
			Low confidence	1212.6	10255.7	11468.3
10	Divided	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	High confidence	75.4118	85	6410
		serpin b12. [swissprot;acc:q96p63]	Low confidence	35.8425	199.549	5.56738
	Subtracted	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]		1211	1593	2804
		myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	High confidence	1637.55	7830.62	6193.07
11	Divided	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Low confidence	34.8539	199.249	5.71669
		serpin b12. [swissprot;acc:q96p63]	High confidence	35.8425	199.549	5.56738
	Subtracted	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		1517.74	5734.28	7252.02
		cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Low confidence	1111.45	4230.36	5341.81
12	Divided	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	High confidence	34.8539	199.249	5.71669
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Low confidence	14.8103	859	58
	Subtracted	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	High confidence	1469.89	5629.62	7099.51
		transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Low confidence	1099.6	31122	30022.4
13	Divided	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	High confidence	29	1363	47
		fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344]	Low confidence	14.21	8.11997	115.385

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.