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

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Showing element 1 to 50 of 77072 in total

Filtered  : 0
Value Type  : Measured

Rank	Interaction Map	description	green	red	network_comparison	Network Comparison Type
1	High confidence	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	85	6325	Subtracted
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	364	36400000	Divided
	Low confidence	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	85	6325	Subtracted
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	364	36400000	Divided
2	High confidence	cab2. [refseq;acc:nm_033419]	174	0.00001	17400000
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	6410	85	6325	Subtracted
	Low confidence	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	89	0.00001	8900000	Divided
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	19621.3	23818.1	4196.8	Subtracted
3	High confidence
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	109	0.00001	10900000	Divided
	Low confidence	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	89		8900000
		nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	7500.75	5106.93	2393.82	Subtracted
4	High confidence	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	89	0.00001	8900000	Divided
		small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	21730	18704	3026	Subtracted
	Low confidence	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	4356	2082	2274
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	89	0.00001	8900000	Divided
5	High confidence	histone h4. [swissprot;acc:p02304]	24446.3	21773.1	2673.2	Subtracted
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	89	0.00001	8900000	Divided
	Low confidence	jumonji protein. [swissprot;acc:q92833]	17.5166		1751660
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	2740.13	485.286	2254.84	Subtracted
6	High confidence	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	89	0.00001	8900000	Divided
		similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	15605.1	13174.7	2430.4	Subtracted
	Low confidence	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	0.00001	13	1300000	Divided
		similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	8836.85	7592.37	1244.48	Subtracted
7	High confidence	sedlin. [swissprot;acc:o14582]	43	0.00001	4300000	Divided
		zinc finger protein 277. [swissprot;acc:q9nrm2]	15605.1	13174.7	2430.4	Subtracted
	Low confidence	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	5898.71	4660.09	1238.62
		tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	0.00001	2.31962	231962	Divided
8	High confidence	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	7500.75	5106.93	2393.82	Subtracted
		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	43	0.00001	4300000	Divided
	Low confidence	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	85	75.4118
		zinc finger protein 277. [swissprot;acc:q9nrm2]	8770.72	7537.89	1232.83	Subtracted
9	High confidence	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	14756	12478	2278
		ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	85	75.4118	Divided
	Low confidence	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	11468.3	10255.7	1212.6	Subtracted
		ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	10.6048	383.762	36.1876	Divided
10	High confidence	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	6410	85	75.4118
		myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	6193.07	7830.62	1637.55	Subtracted
	Low confidence	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	2804	1593	1211
		serpin b12. [swissprot;acc:q96p63]	5.56738	199.549	35.8425	Divided
11	High confidence	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	7252.02	5734.28	1517.74	Subtracted
		serpin b12. [swissprot;acc:q96p63]	5.56738	199.549	35.8425	Divided
	Low confidence	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	5341.81	4230.36	1111.45	Subtracted
		hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	5.71669	199.249	34.8539	Divided
12	High confidence	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	7099.51	5629.62	1469.89	Subtracted
		hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	5.71669	199.249	34.8539	Divided
	Low confidence	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	58	859	14.8103
		transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	30022.4	31122	1099.6	Subtracted
13	High confidence	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	47	1363	29	Divided
					1316	Subtracted

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.