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

Results: HTML CSV LaTeX

Showing element 61824 to 61873 of 66312 in total

Interaction Map  : Low confidence
Filtered  : 1

Rank	description	Hugo	Value Type	Network Comparison Type	red	green	network_comparison
4500	vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270]	VPS11	Squared	Divided	41530.4	40679.8	1.02091
4501	60s ribosomal protein l21. [swissprot;acc:p46778]	no value	Ranked		198.901	197.192	1.00867
	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]	ACADVL	Squared	Subtracted	48280.4	49179.6	899.2
	amiloride-sensitive brain sodium channel bnac2 (amiloride-sensitive cation channel neuronal 2). [swissprot;acc:p78348]	ACCN2	Measured		7467.12	7614.3	147.18
	dgcr8 protein (digeorge syndrome critical region 8). [swissprot;acc:q8wyq5]	DGCR8	Squared	Divided	52462.1	53559.3	1.02091
	homeobox protein meis1. [swissprot;acc:o00470]	MEIS1	Ranked	Subtracted	202.904	201.186	1.718
	nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594]	HRB	Rooted	Divided	74.1073	75.7922	1.02274
	skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192]	FHL2	Measured		7642.49	7785.75	1.01875
	transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112]	HRAS	Rooted	Subtracted	75.1619	76.8014	1.6395
4502	40s ribosomal protein s23. [swissprot;acc:p39028]	RPS23	Ranked		209.371	211.088	1.717
	6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [swissprot;acc:q03393]	PTS	Rooted	Divided	74.1081	75.7917	1.02272
	amiloride-sensitive brain sodium channel bnac1 (amiloride-sensitive cation channel neuronal 1) (bnc1) (degenerin channel mdeg). [swissprot;acc:q16515]	ACCN1	Measured	Subtracted	7467.11	7614.29	147.18
	hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500]	HTATSF1	Squared		44287.6	43389.1	898.5
	interleukin enhancer binding factor 2; nuclear factor of activated t-cells, 45-kda. [refseq;acc:nm_004515]	ILF2	Measured	Divided	8204.38	8357.76	1.01869
	pendrin (sodium-independent chloride/iodide transporter). [swissprot;acc:o43511]	SLC26A4	Ranked		198.901	197.192	1.00867
	putative nfkb activating protein hnlf. [refseq;acc:nm_182547]	TMED4	Rooted	Subtracted	74.6906	76.3273	1.6367
	ribonuclease iii (ec 3.1.26.3) (rnase iii) (p241). [swissprot;acc:q9nrr4]	RNASEN	Squared	Divided	52462.1	53559.3	1.02091
4503	ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170]	AIP	Measured		8303.78	8458.91	1.01868
	alpha-methylacyl-coa racemase (ec 5.1.99.4) (2-methylacyl-coa racemase). [swissprot;acc:q9uhk6]	C1QTNF3		Subtracted	8346.83	8494.01	147.18
	cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238]	no value	Squared		30878.8	29982.3	896.5
	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]		Ranked		201.675	203.389	1.714
	nadh-ubiquinone oxidoreductase b18 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b18) (ci-b18) (cell adhesion protein sqm1). [swissprot;acc:p17568]	NDUFB7	Squared	Divided	52462.1	53559.3	1.02091
	solute carrier family 26 member 6 (pendrin-like protein 1) (pendrin l1). [swissprot;acc:q9bxs9]	no value	Ranked		198.901	197.192	1.00867
	stathmin (phosphoprotein p19) (pp19) (oncoprotein 18) (op18) (leukemia-associated phosphoprotein p18) (pp17) (prosolin) (metablastin) (pr22 protein). [swissprot;acc:p16949]	STMN1	Rooted		74.1081	75.7917	1.02272
	transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [swissprot;acc:q15014]	MORF4L2		Subtracted	71.6555	73.2903	1.6348
4504	aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9]	AIPL1	Measured	Divided	8302.46	8457.37	1.01866
	atp synthase d chain, mitochondrial (ec 3.6.3.14) (my032 protein). [swissprot;acc:o75947]	ATP5H		Subtracted	9325.94	9178.79	147.15
	glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434]	no value	Ranked	Divided	201.956	200.222	1.00866
	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13]	SHOC2	Rooted	Subtracted	75.1763	76.811	1.6347
	set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197]	SMYD2	Squared		30878.8	29982.3	896.5
	stathmin 2 (scg10 protein) (superior cervical ganglion-10 protein). [swissprot;acc:q93045]	STMN2	Rooted	Divided	74.1081	75.7917	1.02272
	transcription factor 12 (transcription factor htf-4) (e-box-binding protein) (dna-binding protein htf4). [swissprot;acc:q99081]	TCF12	Ranked	Subtracted	204.379	202.666	1.713
	zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822]	HIVEP1	Squared	Divided	52462.1	53559.3	1.02091
4505	60s ribosomal protein l26. [swissprot;acc:q02877]	RPL26	Ranked		207.061	208.837	1.00858
	atp synthase lipid-binding protein, mitochondrial precursor (ec 3.6.3.14) (atp synthase proteolipid p3) (atpase protein 9) (atpase subunit c). [swissprot;acc:p48201]	ATP5G3	Measured	Subtracted	8346.47	8493.59	147.12
	cgthba protein (-14 gene protein). [swissprot;acc:q12980]	C16orf35	Rooted	Divided	74.1081	75.7917	1.02272
	fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467]	FBP1	Squared		43657.5	44569.5	1.02089
	importin 13; ran binding protein 13. [refseq;acc:nm_014652]	IPO13	Ranked	Subtracted	201.994	200.284	1.71
	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]	no value	Rooted		75.177	76.8115	1.6345
	set and mynd domain containing protein 1. [sptrembl;acc:q8nb12]	SMYD1	Squared		30878.8	29982.3	896.5
	signal recognition particle 72 kda protein (srp72). [swissprot;acc:o76094]	SRP72	Measured	Divided	8440.36	8597.21	1.01858
4506	butyrate-induced transcript 1. [refseq;acc:nm_016395]	PTPLAD1	Rooted		74.1081	75.7917	1.02272
	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	CSTF3		Subtracted	75.8084	77.442	1.6336
	heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597]	HNRPF	Squared		38980.3	38084.4	895.9
	homeobox protein meis1. [swissprot;acc:o00470]	MEIS1	Ranked	Divided	202.904	201.186	1.00854
	peroxisome assembly factor-1 (paf-1) (peroxin-2) (peroxisomal membrane protein 3) (35 kda peroxisomal membrane protein). [swissprot;acc:p28328]	PXMP3	Measured		7630.23	7771.57	1.01852
	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]	SEC61A1		Subtracted	7466.38	7613.31	146.93
	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052]	ARHGEF6	Squared	Divided	40421.6	39594.9	1.02088
	solute carrier family 26, member 9 isoform b; anion transporter/exchanger-9. [refseq;acc:nm_134325]	SLC26A9	Ranked	Subtracted	198.901	197.192	1.709
4507	ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]	ARIH2	Measured		8313.07	8459.88	146.81

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.