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

Results: HTML CSV LaTeX

Showing element 130 to 179 of 515 in total

Network Comparison Type  : Subtracted
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
red  : 0
green  : 0
network_comparison  : 0

Rank	description	Hugo
2885	carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [swissprot;acc:p23786]	CPT2
2886	complement component c8 alpha chain precursor. [swissprot;acc:p07357]	C8A
2887	mothers against decapentaplegic homolog interacting protein (madh-interacting protein) (smad anchor for receptor activation) (receptor activation anchor) (hsara) (novel serine protease) (nsp). [swissprot;acc:o95405]	ZFYVE9
2888	eukaryotic initiation factor 4a-ii (eif-4a-ii) (eif4a-ii). [swissprot;acc:q14240]	EIF4A2
2889	udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133]	UGT2B4
2890	ccr4-not transcription complex, subunit 8 (caf1-like protein) (califp). [swissprot;acc:q9uff9]	CNOT8
2891	putative mitochondrial solute carrier; hypothetical protein npd016; putative mitochondrial solute carrier. [refseq;acc:nm_031212]	SLC25A28
2892	cyclin-dependent kinase (cdc2-like) 11; death-preventing kinase. [refseq;acc:nm_015076]	CDC2L6
2893	atp synthase coupling factor 6, mitochondrial precursor (ec 3.6.3.14) (f6). [swissprot;acc:p18859]	ATP5J
2894	transcription initiation factor iie, alpha subunit (tfiie-alpha) (general transcription factor iie 56 kda subunit). [swissprot;acc:p29083]	GTF2E1
2895	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]	no value
2896	bone morphogenetic protein 6 precursor (bmp-6). [swissprot;acc:p22004]	BMP6
2897	serine/threonine kinase 38 like. [refseq;acc:nm_015000]	no value
2898	likely ortholog of mouse c-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 13; c-type lectin 13; likely ortholog of rat kupffer cell c-type lectin receptor. [refseq;acc:nm_173535]	CLEC4F
2899	sparc-like protein 1 precursor (high endothelial venule protein) (hevin) (mast 9). [swissprot;acc:q14515]	SPARCL1
2900	schwannomin interacting protein 1. [refseq;acc:nm_014575]	SCHIP1
2901	casein kinase i, gamma 3 isoform (ec 2.7.1.-) (cki-gamma 3). [swissprot;acc:q9y6m4]	CSNK1G3
2902	ubiquitin protein ligase. [refseq;acc:nm_130466]	UBE3B
2903	protein transport protein sec24d (sec24-related protein d). [swissprot;acc:o94855]	SEC24D
2904	6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [swissprot;acc:q03393]	PTS
2905	integrin beta-1 precursor (fibronectin receptor beta subunit) (cd29 antigen) (integrin vla-4 beta subunit). [swissprot;acc:p05556]	ITGB1
2906	thousand and one amino acid protein kinase. [refseq;acc:nm_004783]	TAOK2
2907	fructose-bisphosphate aldolase a (ec 4.1.2.13) (muscle-type aldolase) (lung cancer antigen ny-lu-1). [swissprot;acc:p04075]	ALDOA
2908	serine/threonine-protein kinase chk1 (ec 2.7.1.-). [swissprot;acc:o14757]	CHEK1
2909	nk6 transcription factor related, locus 2; nk homeobox family 6, b; glial and testis-specific homeobox protein; homeobox 6b. [refseq;acc:nm_177400]	NKX6-2
2910	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	no value
2911	bup protein. [refseq;acc:nm_012071]	COMMD3
2912	inositol polyphosphate-5-phosphatase; phosphatidylinositol polyphosphate 5-phosphatase type iv; phosphatidylinositol (4,5) bisphosphate 5-phosphatase. [refseq;acc:nm_019892]	INPP5E
2913	au rna-binding protein/enoyl-coenzyme a hydratase precursor; au rna-binding protein/enoyl-coenzyme a hydratase; 3-methylglutaconyl-coa hydratase; mga type i. [refseq;acc:nm_001698]	AUH
2914	lactamase, beta 2. [refseq;acc:nm_016027]	LACTB2
2915	mitochondrial solute carrier protein. [refseq;acc:nm_016612]	SLC25A37
2916	ribose-phosphate pyrophosphokinase i (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase i) (ppribp) (prs-i). [swissprot;acc:p09329]	PRPS1L1
2917	t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227]	CCT6A
2918	nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323]	GBAS
2919	glycine receptor alpha-1 chain precursor (glycine receptor 48 kda subunit) (strychnine binding subunit). [swissprot;acc:p23415]	GLRA1
2920	glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311]	GLRA3
2921	ell-associated factor 2; uncharacterized bone marrow protein bm040; testosterone regulated apoptosis inducer and tumor suppressor. [refseq;acc:nm_018456]	EAF2
2922	10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891]	ALDH1L1
2923	transmembrane protein 4. [refseq;acc:nm_014255]	TMEM4
2924	rcd1 required for cell differentiation1 homolog; protein involved in sexual development; rcd1 (required for cell differentiation, s.pombe) homolog 1. [refseq;acc:nm_005444]	RQCD1
2925	ras-related protein ral-b. [swissprot;acc:p11234]	RALB
2926	dual specificity protein phosphatase 11 (ec 3.1.3.48) (rna/rnp complex-intereracting phosphatase) (phosphatase that interacts with rna/rnp complex 1). [swissprot;acc:o75319]	DUSP11
2927	wd-repeat containing protein ciao 1. [swissprot;acc:o76071]	CIAO1
2928	calmodulin. [swissprot;acc:p02593]	no value
2929	lysosomal trafficking regulator (beige homolog). [swissprot;acc:q99698]	LYST
2930	interleukin enhancer binding factor 2; nuclear factor of activated t-cells, 45-kda. [refseq;acc:nm_004515]	ILF2
2931	tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753]	TPM3
2932	pogo transposable element with znf domain isoform 1. [refseq;acc:nm_015100]	POGZ
2933	semaphorin 6c precursor (semaphorin y) (sema y). [swissprot;acc:q9h3t2]	SEMA6C
2934	protoporphyrinogen oxidase (ec 1.3.3.4) (ppo). [swissprot;acc:p50336]	PPOX

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.