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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Filtered  : 0
Value Type  : Measured

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

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.