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 3062 to 3111 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
3062	SPARC	sparc precursor (secreted protein acidic and rich in cysteine) (osteonectin) (on) (basement membrane protein bm-40). [swissprot;acc:p09486]
3063	MRPS30	mitochondrial 28s ribosomal protein s30 (s30mt) (mrp-s30) (programmed cell death protein 9) (bm047). [swissprot;acc:q9np92]
3064	C7	complement component c7 precursor. [swissprot;acc:p10643]
3065	WISP3	wnt1 inducible signaling pathway protein 3 isoform 1; wnt-1 signaling pathway protein 3; wnt1 signaling pathway protein 3; wnt-1 inducible signaling pathway protein 3. [refseq;acc:nm_003880]
3066	VEGFA	vascular endothelial growth factor a precursor (vegf-a) (vascular permeability factor) (vpf). [swissprot;acc:p15692]
3067	no value	retinoic acid receptor rxr-beta. [swissprot;acc:p28702]
3068	HECA	headcase homolog; hhdc for homolog of drosophila headcase. [refseq;acc:nm_016217]
3069	BMP5	bone morphogenetic protein 5 precursor (bmp-5). [swissprot;acc:p22003]
3070	MDGA1	mam domain containing glycosylphosphatidylinositol anchor 1; glycosyl-phosphatidyl-inositol-mam. [refseq;acc:nm_153487]
3071	STK38	serine/threonine kinase 38; serine threonine protein kinase. [refseq;acc:nm_007271]
3072	PAK1IP1	pak1 interacting protein 1; pak1-interacting protein; pak/plc-interacting protein 1. [refseq;acc:nm_017906]
3073	RWDD1	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]
3074	NT5DC3	tu12b1-ty protein. [refseq;acc:nm_016575]
3075	USP5	ubiquitin carboxyl-terminal hydrolase 5 (ec 3.1.2.15) (ubiquitin thiolesterase 5) (ubiquitin-specific processing protease 5) (deubiquitinating enzyme 5) (isopeptidase t). [swissprot;acc:p45974]
3076	no value	placental protein 11 precursor (ec 3.4.21.-) (pp11). [swissprot;acc:p21128]
3077	H2AFJ	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
3078	CREBL2	camp responsive element binding protein-like 2. [refseq;acc:nm_001310]
3079	CYP27B1	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]
3080	no value	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]
3081	PTPMT1	nadh-ubiquinone oxidoreductase 30 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-30kd) (ci-30kd). [swissprot;acc:o75489]
3082	CRYAB	alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511]
3083	GLRB	glycine receptor beta chain precursor (glycine receptor 58 kda subunit). [swissprot;acc:p48167]
3084	MAP2K1IP1	mitogen-activated protein kinase kinase 1 interacting protein 1 (mek binding partner 1) (mp1) (pro2783). [swissprot;acc:q9uha4]
3085	UGT2B10	udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537]
3086	no value	udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855]
3087	ALDOC	fructose-bisphosphate aldolase c (ec 4.1.2.13) (brain-type aldolase). [swissprot;acc:p09972]
3088	YWHAE	14-3-3 protein epsilon (mitochondrial import stimulation factor l subunit) (protein kinase c inhibitor protein-1) (kcip-1) (14-3-3e). [swissprot;acc:p42655]
3089	PRKAR1A	camp-dependent protein kinase type i-alpha regulatory chain (tissue- specific extinguisher-1) (tse1). [swissprot;acc:p10644]
3090	EZH1	enhancer of zeste homolog 1 (enx-2). [swissprot;acc:q92800]
3091	MLX	transcription factor-like protein 4 (max-like bhlhzip protein) (bigmax protein) (mlx). [swissprot;acc:q9uh92]
3092	DRG2	developmentally regulated gtp-binding protein 2 (drg 2). [swissprot;acc:p55039]
3093	no value	ptd016 protein. [refseq;acc:nm_016125]
3094	UBE2S	ubiquitin-conjugating enzyme e2-24 kda (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2-epf5). [swissprot;acc:q16763]
3095	C10orf137	erythroid differentiation-related factor 1. [refseq;acc:nm_015608]
3096	NPM3	nucleoplasmin 3. [swissprot;acc:o75607]
3097	SEC23IP	sec23-interacting protein p125; phospholipase. [refseq;acc:nm_007190]
3098	EZH2	enhancer of zeste homolog 2 (enx-1). [swissprot;acc:q15910]
3099	CAV1	caveolin-1. [swissprot;acc:q03135]
3100	no value	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]
3101		gamma-interferon inducible lysosomal thiol reductase precursor (gamma-interferon-inducible protein ip-30). [swissprot;acc:p13284]
3102	C19orf56	protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284]
3103	LIG1	dna ligase i (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p18858]
3104	SNORD23	glioma tumor suppressor candidate region gene 2 protein (p60). [swissprot;acc:q9nzm5]
3105	TGFB1	transforming growth factor beta 1 precursor (tgf-beta 1). [swissprot;acc:p01137]
3106	PTOV1	prostate tumor overexpressed gene 1; prostate tumor over expressed gene 1. [refseq;acc:nm_017432]
3107	LYL1	lyl-1 protein (lymphoblastic leukemia derived sequence 1). [swissprot;acc:p12980]
3108	SNX16	sorting nexin 16. [swissprot;acc:p57768]
3109	WISP1	wnt1 inducible signaling pathway protein 1 isoform 1 precursor; wnt-1 signaling pathway protein 1; wnt1 signaling pathway protein 1; wnt-1 inducible signaling pathway protein 1. [refseq;acc:nm_003882]
3110	RAB2A	ras-related protein rab-2a. [swissprot;acc:p08886]
3111	STK3	serine/threonine protein kinase 3 (ec 2.7.1.37) (ste20-like kinase mst2) (mst-2) (mammalian ste20-like protein kinase 2) (serine/threonine protein kinase krs-1). [swissprot;acc:q13188]

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.