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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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Filtered	Gene	Rank	Value Type	description	green	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	description	green	Interaction Map	Network Comparison Type	red	network_comparison
1	Measured	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	High confidence	Subtracted	85	6325
				Low confidence
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	High confidence	Divided	364	36400000
				Low confidence
	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	High confidence		4294	3.70633
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883		Subtracted	8906	12977
				Low confidence
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977		Divided	5865	2.55362
	Squared	cab2. [refseq;acc:nm_033419]	7.16592	High confidence		0.00001	716592
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	1.87479	Low confidence			187479
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	160184	High confidence	Subtracted	232467	72283
				Low confidence
	Rooted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	60.0707	High confidence		9.20014	50.8706
				Low confidence
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	High confidence	Divided	19.0788	1907880
				Low confidence
2	Measured	cab2. [refseq;acc:nm_033419]	174	High confidence		0.00001	17400000
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	89	Low confidence			8900000
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	6410	High confidence	Subtracted	85	6325
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	19621.3	Low confidence		23818.1	4196.8
	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	High confidence		4294	11621
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883	Low confidence	Divided	8906	2.45711
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	High confidence		5865	2.55362
		neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	20617	Low confidence	Subtracted	9607	11010
	Squared	histone h4. [swissprot;acc:p02304]	345123	High confidence		273623	71500
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	1.87479	Low confidence	Divided	0.00001	187479
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001	High confidence		5.61325	561325
		transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	386144	Low confidence	Subtracted	414704	28560
	Rooted	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	9.43398		Divided	0.00001	943398
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	60.0707	High confidence	Subtracted	9.20014	50.8706
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	7.61577	Low confidence		29.3087	21.6929
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001	High confidence	Divided	12.4097	1240970
3	Measured	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	89	Low confidence		0.00001	8900000
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	19621.3	High confidence	Subtracted	23818.1	4196.8
		nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	7500.75	Low confidence		5106.93	2393.82
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	109	High confidence	Divided	0.00001	10900000
	Ranked	cab2. [refseq;acc:nm_033419]	10950		Subtracted	21866	10916
		neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	20617	Low confidence	Divided	9607	2.14604
		neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]			Subtracted		11010
		nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	11083.9	High confidence	Divided	4475.84	2.47638
	Squared	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	170628		Subtracted	135280	35348
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	1.87479	Low confidence	Divided	0.00001	187479
		rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565]	197937		Subtracted	220988	23051
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001	High confidence	Divided	5.61325	561325
	Rooted	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	6.85565		Subtracted	36.9188	30.0631
		anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	66	Low confidence		45.6289	20.3711
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	9.43398		Divided	0.00001	943398
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001	High confidence		12.4097	1240970
4	Measured	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	4356	Low confidence	Subtracted	2082	2274
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	89		Divided	0.00001	8900000

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.