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

Results: HTML CSV LaTeX

Showing element 401 to 450 of 77072 in total

Rank	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison
13	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	Ranked	Divided	High confidence	0	5210.5	9264.5	1.77804
	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	Measured	Subtracted	Low confidence	1	15464.1	17572.7	2108.6
	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433]		Divided			1927.68	2959.19	1.5351
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Squared	Subtracted	High confidence	0	1.73869	19295.9	19294.2
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]				1	219048	129762	89286
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Measured				21591.5	27904.5	6313
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Ranked	Divided	Low confidence		37.9984	29.1831	1.30207
		Rooted	Subtracted			186.878	204.057	17.179
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Ranked	Divided	High confidence		288.754	212.554	1.3585
			Subtracted	Low confidence		255.046	202.362	52.684
	rhomboid-related protein 1 (ec 3.4.21.-) (rrp) (rhomboid-like protein 1). [swissprot;acc:o75783]	Squared				281799	228277	53522
	similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]				0	38389.3	49559.8	11170.5
	sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796]	Ranked	Divided			7435.56	12191.6	1.63963
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Measured	Subtracted			2961.07	3953.32	992.25
	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	Squared	Divided			0.00219609	0.00001	219.609
	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	Rooted				17.0721	2.21126	7.72053
14	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	Ranked	Subtracted		1	286.396	238.476	47.92
	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	Measured		High confidence	0	10817.1	12125.1	1308
	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Squared	Divided	Low confidence	1	7744.68	4959.41	1.56161
	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Ranked	Subtracted		0	13730.5	8257	5473.5
		Squared	Divided	High confidence		1.73869	19295.9	11098
		Rooted		Low confidence		9.20014	60.0707	6.52932
	block 23. [sptrembl;acc:q8nhw5]	Squared	Subtracted			38133.9	49224.6	11090.7
	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Measured	Divided	High confidence		130.512	6.50325	20.0687
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Ranked			1	56.6768	75.3531	1.32952
	cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318]	Rooted		Low confidence		39.2489	52.5401	1.33864
	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]		Subtracted	High confidence	0	39.9124	52.9528	13.0404
	dystrophin. [swissprot;acc:p11532]	Ranked	Divided			10232.5	18054.8	1.76446
	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]	Measured		Low confidence		0.00001	59	5900000
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Ranked	Subtracted	High confidence	1	266.863	336.191	69.328
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Squared		Low confidence		122475	159767	37292
	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	Measured				15464.1	17572.7	2108.6
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Squared		High confidence		219048	129762	89286
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		Divided	Low confidence	0	174.646	0.796213	219.346
	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Measured	Subtracted	High confidence	1	21591.5	27904.5	6313
	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750]	Rooted	Divided		0	0.00001	4.24264	424264
	protein cgi-147. [swissprot;acc:q9y3e5]	Squared	Subtracted			75129.2	94178	19048.8
	protein kinase, lysine deficient 3. [refseq;acc:nm_020922]	Rooted		Low confidence		10.6742	21.7584	11.0842
	ptd016 protein. [refseq;acc:nm_016125]	Ranked	Divided			18050	11234	1.60673
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Measured		High confidence	1	398.5	1281.5	3.21581
		Squared				37.5863	388.696	10.3414
		Rooted				19.9625	35.798	1.79326
	rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565]	Measured	Subtracted	Low confidence	0	17235.5	16295.1	940.4
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Rooted		High confidence	1	80.4705	101.526	21.0555
	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]	Measured	Divided	Low confidence		1972.65	2998.1	1.51983
	ubiquitin protein ligase. [refseq;acc:nm_130466]	Ranked	Subtracted	High confidence	0	7523	15339.2	7816.2
	vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]		Divided	Low confidence	1	37.9984	29.1831	1.30207
		Rooted	Subtracted			186.878	204.057	17.179
15	adenomatous polyposis coli like. [refseq;acc:nm_005883]	Ranked	Divided		0	12074.1	7597.61	1.5892
	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	Rooted	Subtracted	High confidence	1	80.4705	101.526	21.0555

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.