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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

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Showing element 1 to 50 of 77072 in total

Filtered  : 0

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

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.