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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Value Type  : Measured
Filtered  : 0

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

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.