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	Hugo	Network Comparison Type	Value Type	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 158 to 207 of 66312 in total

Filtered  : 1

Rank	description	Hugo	Network Comparison Type	Value Type	Interaction Map	red	green	network_comparison
10	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	TOB1	Divided	Squared	High confidence	37.5863	388.696	10.3414
				Rooted		19.9625	35.798	1.79326
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	XAB1	Subtracted			51.6817	29.5127	22.169
11	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	MRPS17	Divided	Squared	Low confidence	106226	192141	1.80879
	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	BEST1		Ranked		37.318	28.4944	1.30966
			Subtracted	Rooted		187.345	204.579	17.234
	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	DAB2IP	Divided	Measured	High confidence	398.5	1281.5	3.21581
				Squared		37.5863	388.696	10.3414
				Rooted		19.9625	35.798	1.79326
	db83 protein. [swissprot;acc:p57088]	TMEM33	Subtracted	Ranked		288	362	74
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	MAGEE2		Squared		219048	129762	89286
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	SLC25A43		Measured		21185	28492	7307
	protein x 0004. [refseq;acc:nm_016301]	ATPBD1C		Rooted		51.6817	29.5127	22.169
	rad50-interacting protein 1. [refseq;acc:nm_021930]	RINT1	Divided	Ranked		337	232	1.45259
	retinoblastoma-associated factor 600. [refseq;acc:nm_020765]	UBR4	Subtracted	Measured	Low confidence	7256.71	9368.87	2112.16
	rhomboid-related protein 4 (ec 3.4.21.-) (ventrhoid transmembrane protein). [swissprot;acc:p58872]	RHBDL3		Squared		281799	228277	53522
	thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652]	JMJD1C	Divided	Measured		1917.64	2950.5	1.53861
	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]	PRSS3		Rooted		32.2231	47.928	1.48738
			Subtracted	Ranked		304.548	246.824	57.724
12	bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061]	TEGT		Squared		281799	228277	53522
	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	ARRB2		Rooted	High confidence	80.4705	101.526	21.0555
	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	CPEB4	Divided	Measured		398.5	1281.5	3.21581
				Squared		37.5863	388.696	10.3414
				Rooted		19.9625	35.798	1.79326
	gbp protein isoform a. [refseq;acc:nm_017870]	TMEM132A		Measured	Low confidence	1921.96	2954.24	1.5371
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	no value	Subtracted	Ranked	High confidence	266.856	336.233	69.377
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]			Measured	Low confidence	15464.1	17572.7	2108.6
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]			Squared	High confidence	219048	129762	89286
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	SLC25A43	Divided		Low confidence	106226	192141	1.80879
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	no value	Subtracted	Measured	High confidence	34190.9	40795.8	6604.9
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	RHOBTB2	Divided	Ranked		337	232	1.45259
	trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477]	PRSS1		Rooted	Low confidence	32.2966	47.9763	1.48549
			Subtracted	Ranked		304.359	246.737	57.622
	vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]	BEST4	Divided			37.3475	28.5242	1.30933
			Subtracted	Rooted		187.325	204.557	17.232
13	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]	CYP27B1	Divided			39.2301	52.5277	1.33896
	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	ARRB1	Subtracted		High confidence	80.4705	101.526	21.0555
	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	CPD	Divided	Squared	Low confidence	395912	242799	1.63062
	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	CPEB3		Measured	High confidence	398.5	1281.5	3.21581
				Squared		37.5863	388.696	10.3414
				Rooted		19.9625	35.798	1.79326
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	GNG12	Subtracted	Ranked		266.856	336.233	69.377
	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	HOXB4		Measured	Low confidence	15464.1	17572.7	2108.6
	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433]	JMJD1A	Divided			1927.68	2959.19	1.5351
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	MAGEA11	Subtracted	Squared	High confidence	219048	129762	89286
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	MYO5B		Measured		21591.5	27904.5	6313
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	no value	Divided	Ranked	Low confidence	37.9984	29.1831	1.30207
			Subtracted	Rooted		186.878	204.057	17.179
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	UFC1	Divided	Ranked	High confidence	288.754	212.554	1.3585
			Subtracted		Low confidence	255.046	202.362	52.684

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
- Hugo is the HGNC identifier if it exists
- 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.