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

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Showing element 1 to 50 of 77072 in total

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Rank	green	Interaction Map	network_comparison	Value Type	description	red	Network Comparison Type
1	0.00001	High confidence	1907880	Rooted	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	19.0788	Divided
			36400000	Measured		364
		Low confidence	1907880	Rooted		19.0788
			36400000	Measured		364
	1.87479		187479	Squared	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0.00001
	7.16592	High confidence	716592		cab2. [refseq;acc:nm_033419]
	60.0707		50.8706	Rooted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	9.20014	Subtracted
		Low confidence
	6410	High confidence	6325	Measured		85
		Low confidence
	14977		2.55362	Ranked	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	5865	Divided
	15915	High confidence	3.70633		adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	4294
	21883		12977		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	8906	Subtracted
		Low confidence
	160184	High confidence	72283	Squared	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	232467
		Low confidence
2	0.00001	High confidence	561325		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	5.61325	Divided
			1240970	Rooted		12.4097
	1.87479	Low confidence	187479	Squared	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0.00001
	7.61577		21.6929	Rooted	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	29.3087	Subtracted
	9.43398		943398		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0.00001	Divided
	60.0707	High confidence	50.8706		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	9.20014	Subtracted
	89	Low confidence	8900000	Measured	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0.00001	Divided
	174	High confidence	17400000		cab2. [refseq;acc:nm_033419]
	6410		6325		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	85	Subtracted
	14977		2.55362	Ranked	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	5865	Divided
	15915		11621		adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	4294	Subtracted
	19621.3	Low confidence	4196.8	Measured	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	23818.1
	20617		11010	Ranked	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	9607
	21883		2.45711		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	8906	Divided
	345123	High confidence	71500	Squared	histone h4. [swissprot;acc:p02304]	273623	Subtracted
	386144	Low confidence	28560		transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	414704
3	0.00001	High confidence	561325		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	5.61325	Divided
			1240970	Rooted		12.4097
	1.87479	Low confidence	187479	Squared	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0.00001
	6.85565	High confidence	30.0631	Rooted	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	36.9188	Subtracted
	9.43398	Low confidence	943398		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0.00001	Divided
	66		20.3711		anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	45.6289	Subtracted
	89		8900000	Measured	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0.00001	Divided
	109	High confidence	10900000		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]
	7500.75	Low confidence	2393.82		nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	5106.93	Subtracted
	10950	High confidence	10916	Ranked	cab2. [refseq;acc:nm_033419]	21866
	11083.9		2.47638		nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	4475.84	Divided
	19621.3		4196.8	Measured	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	23818.1	Subtracted
	20617	Low confidence	2.14604	Ranked	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	9607	Divided
			11010		neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]		Subtracted
	170628	High confidence	35348	Squared	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	135280
	197937	Low confidence	23051		rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565]	220988
4	0		19.0788	Rooted	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	19.0788
	0.823905		82390.5	Squared	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]	0.00001	Divided

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.