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

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Showing element 3113 to 3162 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
3113	NUTF2	nuclear transport factor 2 (ntf-2) (placental protein 15) (pp15). [swissprot;acc:p13662]
3114	TSC22D1	regulatory protein tsc-22 (tgfb stimulated clone 22 homolog). [swissprot;acc:q15714]
3115	STK24	serine/threonine protein kinase 24 (ec 2.7.1.37) (ste20-like kinase mst3) (mst-3) (mammalian ste20-like protein kinase 3). [swissprot;acc:q9y6e0]
3116	CAB39L	mo25-like protein. [swissprot;acc:q9h9s4]
3117	FNDC3A	ba203i16.1 (hypothetical protein kiaa0970). [sptrembl;acc:q9h1w1]
3118	SMS	spermine synthase (ec 2.5.1.22) (spermidine aminopropyltransferase) (spmsy). [swissprot;acc:p52788]
3119	no value	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]
3120	SCML2	sex comb on midleg-like 2; sex comb on midleg like 2. [refseq;acc:nm_006089]
3121	GLRA2	glycine receptor alpha-2 chain precursor. [swissprot;acc:p23416]
3122	PRPS2	ribose-phosphate pyrophosphokinase ii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase ii) (ppribp) (prs-ii). [swissprot;acc:p11908]
3123	VAPA	vesicle-associated membrane protein-associated protein a (vamp- associated protein a) (vamp-a) (vap-a) (33 kda vamp-associated protein) (vap-33). [swissprot;acc:q9p0l0]
3124	SAMHD1	sam domain and hd domain-containing protein 1 (dendritic cell-derived ifng-induced protein) (dcip) (monocyte protein 5) (mop-5). [swissprot;acc:q9y3z3]
3125	POFUT1	gdp-fucose protein o-fucosyltransferase 1 precursor (ec 2.4.1.221) (peptide o-fucosyltransferase) (o-fuct-1). [swissprot;acc:q9h488]
3126	PLCB4	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4 (ec 3.1.4.11) (phosphoinositide phospholipase c) (plc-beta-4) (phospholipase c-beta-4). [swissprot;acc:q15147]
3127	SEC23B	protein transport protein sec23b (sec23-related protein b). [swissprot;acc:q15437]
3128	BMP7	bone morphogenetic protein 7 precursor (bmp-7) (osteogenic protein 1) (op-1). [swissprot;acc:p18075]
3129	CSTF1	cleavage stimulation factor, 50 kda subunit (cstf 50 kda subunit) (cf-1 50 kda subunit). [swissprot;acc:q05048]
3130	PFDN4	prefoldin subunit 4 (protein c-1). [swissprot;acc:q9nqp4]
3131	C20orf24	protein c20orf24 (rab5-interacting protein) (rip5) (pnas-11). [swissprot;acc:q9buv8]
3132	R3HDML	r3h domain (binds single-stranded nucleic acids) containing-like. [refseq;acc:nm_178491]
3133	IFT52	ngd5 protein homolog (cgi-53). [swissprot;acc:q9y366]
3134	RABGGTA	rab geranylgeranyltransferase alpha subunit (ec 2.5.1.-) (rab geranyl- geranyltransferase alpha subunit) (rab gg transferase alpha) (rab ggtase alpha). [swissprot;acc:q92696]
3135	SEC23A	protein transport protein sec23a (sec23-related protein a). [swissprot;acc:q15436]
3136	VRK1	vaccinia related kinase 1; vaccinia-related kinase-1. [refseq;acc:nm_003384]
3137	CDKL1	serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532]
3138	C14orf124	hcdi protein. [refseq;acc:nm_020195]
3139	BRD1	bromodomain-containing protein 1 (br140-like protein). [swissprot;acc:o95696]
3140	MYH9	myosin heavy chain, nonmuscle type a (cellular myosin heavy chain, type a) (nonmuscle myosin heavy chain-a) (nmmhc-a). [swissprot;acc:p35579]
3141	TTLL1	tubulin tyrosine ligase-like protein 1. [swissprot;acc:o95922]
3142	PACSIN2	protein kinase c and casein kinase substrate in neurons protein 2. [swissprot;acc:q9unf0]
3143	PICK1	prkca-binding protein (protein kinase c-alpha binding protein) (protein interacting with c kinase 1). [swissprot;acc:q9nrd5]
3144	HMG1L10	high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]
3145	UPB1	beta-ureidopropionase (ec 3.5.1.6) (beta-alanine synthase) (n-carbamoyl-beta-alanine amidohydrolase) (bup-1). [swissprot;acc:q9ubr1]
3146	DERL3	putative nadh oxidoreductase complex i subunit homolog. [sptrembl;acc:q96q80]
3147	HSD3B7	3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193]
3148	no value	muts protein homolog 5. [swissprot;acc:o43196]
3149	BRPF3	bromodomain and phd finger-containing protein 3 (fragment). [swissprot;acc:q9uld4]
3150	CRISP3	cysteine-rich secretory protein-3 precursor (crisp-3) (sgp28 protein). [swissprot;acc:p54108]
3151	MSH2	dna mismatch repair protein msh2. [swissprot;acc:p43246]
3152	HDAC6	histone deacetylase 6 (hd6). [swissprot;acc:q9ubn7]
3153	LRRFIP2	leucine rich repeat (in flii) interacting protein 2. [refseq;acc:nm_006309]
3154	NUP50	nucleoporin 50 kda (nuclear pore-associated protein 60 kda-like) (pro1146). [swissprot;acc:q9ukx7]
3155	TGFB2	transforming growth factor beta 2 precursor (tgf-beta 2) (glioblastoma-derived t-cell suppressor factor) (g-tsf) (bsc-1 cell growth inhibitor) (polyergin) (cetermin). [swissprot;acc:p08112]
3156	TEKT2	tektin 2 (tektin-t) (testicular tektin b1-like protein). [swissprot;acc:q9uif3]
3157	SCFD1	vesicle transport-related protein isoform a; vesicle transport-related protein. [refseq;acc:nm_016106]
3158	ITGA6	integrin alpha-6 precursor (vla-6) (cd49f). [swissprot;acc:p23229]
3159	TNRC6A	trinucleotide repeat containing 6; edie; gw182 autoantigen. [refseq;acc:nm_014494]
3160	CCNK	cyclin k. [swissprot;acc:o75909]
3161	BRAP	brca1 associated protein. [refseq;acc:nm_006768]
3162	PEBP1	phosphatidylethanolamine-binding protein (pebp) (prostatic binding protein) (hcnppp) (neuropolypeptide h3) (raf kinase inhibitor protein) (rkip) [contains: hippocampal cholinergic neurostimulating peptide (hcnp)]. [swissprot;acc:p30086]

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.