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

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Showing element 1 to 50 of 77072 in total

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Rank	Value Type	green	description	Interaction Map	Network Comparison Type	red	network_comparison
1	Measured	0.00001	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	High confidence	Divided	364	36400000
				Low confidence
		6410	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	High confidence	Subtracted	85	6325
				Low confidence
	Ranked	14977	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		Divided	5865	2.55362
		15915	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	High confidence		4294	3.70633
		21883	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		Subtracted	8906	12977
				Low confidence
	Squared	1.87479	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Divided	0.00001	187479
		7.16592	cab2. [refseq;acc:nm_033419]	High confidence			716592
		160184	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		Subtracted	232467	72283
				Low confidence
	Rooted	0.00001	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	High confidence	Divided	19.0788	1907880
				Low confidence
		60.0707	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	High confidence	Subtracted	9.20014	50.8706
				Low confidence
2	Measured	89	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Divided	0.00001	8900000
		174	cab2. [refseq;acc:nm_033419]	High confidence			17400000
		6410	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]		Subtracted	85	6325
		19621.3	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Low confidence		23818.1	4196.8
	Ranked	14977	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	High confidence	Divided	5865	2.55362
		15915	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]		Subtracted	4294	11621
		20617	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Low confidence		9607	11010
		21883	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		Divided	8906	2.45711
	Squared	0.00001	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	High confidence		5.61325	561325
		1.87479	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Low confidence		0.00001	187479
		345123	histone h4. [swissprot;acc:p02304]	High confidence	Subtracted	273623	71500
		386144	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Low confidence		414704	28560
	Rooted	0.00001	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	High confidence	Divided	12.4097	1240970
		7.61577	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Low confidence	Subtracted	29.3087	21.6929
		9.43398	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Divided	0.00001	943398
		60.0707	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	High confidence	Subtracted	9.20014	50.8706
3	Measured	89	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Low confidence	Divided	0.00001	8900000
		109	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	High confidence			10900000
		7500.75	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Low confidence	Subtracted	5106.93	2393.82
		19621.3	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	High confidence		23818.1	4196.8
	Ranked	10950	cab2. [refseq;acc:nm_033419]			21866	10916
		11083.9	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]		Divided	4475.84	2.47638
		20617	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Low confidence		9607	2.14604
			neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]		Subtracted		11010
	Squared	0.00001	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	High confidence	Divided	5.61325	561325
		1.87479	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Low confidence		0.00001	187479
		170628	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	High confidence	Subtracted	135280	35348
		197937	rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565]	Low confidence		220988	23051
	Rooted	0.00001	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	High confidence	Divided	12.4097	1240970
		6.85565	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]		Subtracted	36.9188	30.0631
		9.43398	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Low confidence	Divided	0.00001	943398
		66	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]		Subtracted	45.6289	20.3711
4	Measured	89	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]		Divided	0.00001	8900000
			homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	High confidence

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.