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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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

Results: HTML CSV LaTeX

Showing element 3008 to 3057 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
red  : 0.00001
green  : 0.00001
network_comparison  : 1

Rank	Hugo	description
3008	NUP214	nuclear pore complex protein nup214 (nucleoporin nup214) (214 kda nucleoporin) (can protein). [swissprot;acc:p35658]
3009	COX6B1	cytochrome c oxidase polypeptide vib (ec 1.9.3.1) (aed). [swissprot;acc:p14854]
3010	UROD	uroporphyrinogen decarboxylase (ec 4.1.1.37) (uro-d) (upd). [swissprot;acc:p06132]
3011	MCM8	dna replication licensing factor mcm8 (minichromosome maintenance 8). [swissprot;acc:q9uja3]
3012	SNRPB	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]
3013	CENPB	major centromere autoantigen b (centromere protein b) (cenp-b). [swissprot;acc:p07199]
3014	SLC25A19	mitochondrial deoxynucleotide carrier (mitochondrial uncoupling protein 1). [swissprot;acc:q9hc21]
3015	NUP85	pericentrin 1; frount; nucleoporin nup75. [refseq;acc:nm_024844]
3016	MRPS7	mitochondrial ribosomal protein s7; 30s ribosomal protein s7 homolog. [refseq;acc:nm_015971]
3017	LRRFIP1	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]
3018	CRISP1	cysteine-rich secretory protein-1 precursor (crisp-1) (acidic epididymal glycoprotein homolog) (aeg-like protein) (arp). [swissprot;acc:p54107]
3019	KLHDC3	testis intracellular mediator protein. [refseq;acc:nm_057161]
3020	PACSIN1	protein kinase c and casein kinase substrate in neurons protein 1. [swissprot;acc:q9by11]
3021	CRISP2	testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562]
3022	NAGK	n-acetylglucosamine kinase (ec 2.7.1.59) (glcnac kinase). [swissprot;acc:q9uj70]
3023	VAPB	vesicle-associated membrane protein-associated protein b/c (vamp- associated protein b/c) (vamp-b/vamp-c) (vap-b/vap-c). [swissprot;acc:o95292]
3024	PIGT	phosphatidylinositol glycan class t precursor. [refseq;acc:nm_015937]
3025	HMG1L1	dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]
3026	SLC36A1	solute carrier family 36 member 1; proton / amino acid symporter; lysosomal amino acid transporter 1. [refseq;acc:nm_078483]
3027	TSFM	elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897]
3028	C13orf1	clll6 protein. [refseq;acc:nm_020456]
3029	DNAI1	dynein intermediate chain 1, axonemal (axonemal dynein intermediate chain 1). [swissprot;acc:q9ui46]
3030	C6orf35	uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452]
3031	SPOP	speckle-type poz protein. [swissprot;acc:o43791]
3032	LYZL1	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]
3033	GPAM	glycerol-3-phosphate acyltransferase, mitochondrial precursor (ec 2.3.1.15) (gpat). [swissprot;acc:q9hcl2]
3034	CRIPT	postsynaptic protein cript; hspc139 protein. [refseq;acc:nm_014171]
3035	TGFB3	transforming growth factor beta 3 precursor (tgf-beta 3). [swissprot;acc:p10600]
3036	PGF	placenta growth factor precursor (plgf). [swissprot;acc:p49763]
3037	VPS4B	skd1 protein (vacuolar sorting protein 4b). [swissprot;acc:o75351]
3038	no value	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]
3039	SET	set protein (hla-dr associated protein ii) (phapii) (phosphatase 2a inhibitor i2pp2a). [swissprot;acc:q01105]
3040	CTGF	connective tissue growth factor precursor (hypertrophic chondrocyte- specific protein 24). [swissprot;acc:p29279]
3041	TTR	transthyretin precursor (prealbumin) (tbpa) (ttr) (attr). [swissprot;acc:p02766]
3042	NR5A2	orphan nuclear receptor nr5a2 (alpha-1-fetoprotein transcription factor) (hepatocytic transcription factor) (b1-binding factor) (hb1f) (cyp7a promoter binding factor). [swissprot;acc:o00482]
3043	TTF2	transcription termination factor, rna polymerase ii; lodestar protein. [refseq;acc:nm_003594]
3044	no value	late endosomal/lysosomal mp1 interacting protein (p14) (hspc003). [swissprot;acc:q9y2q5]
3045	MSH6	dna mismatch repair protein msh6 (muts-alpha 160 kda subunit) (g/t mismatch binding protein) (gtbp) (gtmbp) (p160). [swissprot;acc:p52701]
3046	CD207	langerhans cell specific c-type lectin. [refseq;acc:nm_015717]
3047	ORC2L	origin recognition complex subunit 2. [swissprot;acc:q13416]
3048	STK25	serine/threonine protein kinase 25 (ec 2.7.1.37) (sterile 20/oxidant stress-response kinase 1) (ste20/oxidant stress response kinase-1) (sok-1) (ste20-like kinase). [swissprot;acc:o00506]
3049	SLC30A3	zinc transporter 3 (znt-3). [swissprot;acc:q99726]
3050	ACVR1	activin receptor type i precursor (ec 2.7.1.37) (actr-i) (serine/threonine-protein kinase receptor r1) (skr1) (activin receptor-like kinase 2) (alk-2) (tgf-b superfamily receptor type i) (tsr-i). [swissprot;acc:q04771]
3051	CYB561D2	putative tumor suppressor 101f6. [refseq;acc:nm_007022]
3052	PDCD10	programmed cell death 10; apoptosis-related protein 15. [refseq;acc:nm_007217]
3053	HGD	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
3054	ZNF346	double-stranded rna-binding zinc finger protein jaz. [refseq;acc:nm_012279]
3055	ATP6V0E1	vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase m9.2 subunit) (v-atpase 9.2 kda membrane accessory protein). [swissprot;acc:o15342]
3056	SEC24A	protein transport protein sec24a (sec24-related protein a) (fragment). [swissprot;acc:o95486]
3057	C9	complement component c9 precursor. [swissprot;acc:p02748]

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.