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

Results: HTML CSV LaTeX

Showing element 475 to 524 of 2060 in total

Network Comparison Type  : Subtracted
red  : 0
green  : 0
network_comparison  : 0
Filtered  : 1

Value Type	Rank	description	Interaction Map
Measured	5021	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]	Low confidence
	5022	histone deacetylase 3 (hd3) (rpd3-2). [swissprot;acc:o15379]
	5023	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]
	5024	spinster-like protein. [sptrembl;acc:q9h2v7]
	5025	thymidine kinase 2, mitochondrial precursor (ec 2.7.1.21) (mt-tk). [swissprot;acc:o00142]
	5026	tigger transposable element derived 6. [refseq;acc:nm_030953]
	5027	runt-related transcription factor 1 (core-binding factor, alpha 2 subunit) (cbf-alpha 2) (acute myeloid leukemia 1 protein) (oncogene aml-1) (polyomavirus enhancer binding protein 2 alpha b subunit) (pebp2-alpha b) (pea2-alpha b) (sl3-3 enhancer factor 1 alpha b subunit) (sl3/akv core-binding factor alpha b subunit). [swissprot;acc:q01196]
	5028	collectin sub-family member 12 isoform i; scavenger receptor with c-type lectin; collectin placenta 1; scavenger receptor class a, member 4. [refseq;acc:nm_130386]
	5029	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]
	5030	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
	5031	cobw-like protein. [refseq;acc:nm_018491]
	5032	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]
	5033	signal recognition particle 14 kda protein (srp14) (18 kda alu rna binding protein). [swissprot;acc:p37108]
	5034	rap1 gtpase-gdp dissociation stimulator 1 (smg p21 stimulatory gdp/gtp exchange protein) (smg gds protein) (exchange factor smggds). [swissprot;acc:p52306]
	5035	solute carrier family 21 member 15 (organic anion transporter polypeptide-related protein 4) (oatp-rp4) (oatprp4). [swissprot;acc:q9h2y9]
	5036	lipin 1. [swissprot;acc:q14693]
	5037	lipin 3 (lipin 3-like) (fragments). [swissprot;acc:q9bqk8]
	5038	myeloblast kiaa0230 (fragment). [sptrembl;acc:q92626]
	5039	testis specific leucine rich repeat protein. [refseq;acc:nm_012472]
	5040	major centromere autoantigen b (centromere protein b) (cenp-b). [swissprot;acc:p07199]
	5041	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]
	5042	n-acetylglucosamine kinase (ec 2.7.1.59) (glcnac kinase). [swissprot;acc:q9uj70]
	5043	transthyretin precursor (prealbumin) (tbpa) (ttr) (attr). [swissprot;acc:p02766]
	5044	late endosomal/lysosomal mp1 interacting protein (p14) (hspc003). [swissprot;acc:q9y2q5]
	5045	langerhans cell specific c-type lectin. [refseq;acc:nm_015717]
	5046	putative tumor suppressor 101f6. [refseq;acc:nm_007022]
	5047	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
	5048	double-stranded rna-binding zinc finger protein jaz. [refseq;acc:nm_012279]
	5049	mitogen-activated protein kinase kinase 1 interacting protein 1 (mek binding partner 1) (mp1) (pro2783). [swissprot;acc:q9uha4]
	5050	lipin 2. [swissprot;acc:q92539]
	5051	sam domain and hd domain-containing protein 1 (dendritic cell-derived ifng-induced protein) (dcip) (monocyte protein 5) (mop-5). [swissprot;acc:q9y3z3]
	5052	tubulin tyrosine ligase-like protein 1. [swissprot;acc:o95922]
	5053	gamma-glutamyltransferase. [sptrembl;acc:q14390]
	5054	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
	5055	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
	5056	putative nadh oxidoreductase complex i subunit homolog. [sptrembl;acc:q96q80]
	5057	leucine rich repeat (in flii) interacting protein 2. [refseq;acc:nm_006309]
	5058	carcinoma related gene. [refseq;acc:nm_016041]
	5059	core-binding factor, beta subunit (cbf-beta) (polyomavirus enhancer binding protein 2 beta subunit) (pebp2-beta) (pea2-beta) (sl3-3 enhancer factor 1 beta subunit) (sl3/akv core-binding factor beta subunit). [swissprot;acc:q13951]
	5060	homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (methyl methanesulfonate (mmf)-inducible fragment protein 1). [swissprot;acc:q15011]
	5061	runt-related transcription factor 3 (core-binding factor, alpha 3 subunit) (cbf-alpha 3) (acute myeloid leukemia 2 protein) (oncogene aml-2) (polyomavirus enhancer binding protein 2 alpha c subunit) (pebp2-alpha c) (pea2-alpha c) (sl3-3 enhancer factor 1 alpha c subunit) (sl3/akv core-binding factor alpha c subunit). [swissprot;acc:q13761]
Ranked	2756	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	High confidence
	2757	nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209]
	2758	nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [swissprot;acc:q9ulw6]
	2759	retinoic acid receptor rxr-alpha. [swissprot;acc:p19793]
	2760	t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [swissprot;acc:q16559]
	2761	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]
	2762	developmentally regulated gtp-binding protein 1 (drg 1). [swissprot;acc:q9y295]
	2763	ring finger protein 3. [refseq;acc:nm_006315]
	2764	ras-related protein rab-11b (gtp-binding protein ypt3). [swissprot;acc:q15907]

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
- 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.