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

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Showing element 1 to 50 of 8289 in total

Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : Low confidence
Filtered  : 1

Rank	description	red	green	network_comparison
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]	0.00001	0.00001	1
5060	homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (methyl methanesulfonate (mmf)-inducible fragment protein 1). [swissprot;acc:q15011]
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]
5058	carcinoma related gene. [refseq;acc:nm_016041]
5057	leucine rich repeat (in flii) interacting protein 2. [refseq;acc:nm_006309]
5056	putative nadh oxidoreductase complex i subunit homolog. [sptrembl;acc:q96q80]
5055	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
5054	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
5053	gamma-glutamyltransferase. [sptrembl;acc:q14390]
5052	tubulin tyrosine ligase-like protein 1. [swissprot;acc:o95922]
5051	sam domain and hd domain-containing protein 1 (dendritic cell-derived ifng-induced protein) (dcip) (monocyte protein 5) (mop-5). [swissprot;acc:q9y3z3]
5050	lipin 2. [swissprot;acc:q92539]
5049	mitogen-activated protein kinase kinase 1 interacting protein 1 (mek binding partner 1) (mp1) (pro2783). [swissprot;acc:q9uha4]
5048	double-stranded rna-binding zinc finger protein jaz. [refseq;acc:nm_012279]
5047	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
5046	putative tumor suppressor 101f6. [refseq;acc:nm_007022]
5045	langerhans cell specific c-type lectin. [refseq;acc:nm_015717]
5044	late endosomal/lysosomal mp1 interacting protein (p14) (hspc003). [swissprot;acc:q9y2q5]
5043	transthyretin precursor (prealbumin) (tbpa) (ttr) (attr). [swissprot;acc:p02766]
5042	n-acetylglucosamine kinase (ec 2.7.1.59) (glcnac kinase). [swissprot;acc:q9uj70]
5041	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]
5040	major centromere autoantigen b (centromere protein b) (cenp-b). [swissprot;acc:p07199]
5039	testis specific leucine rich repeat protein. [refseq;acc:nm_012472]
5038	myeloblast kiaa0230 (fragment). [sptrembl;acc:q92626]
5037	lipin 3 (lipin 3-like) (fragments). [swissprot;acc:q9bqk8]
5036	lipin 1. [swissprot;acc:q14693]
5035	solute carrier family 21 member 15 (organic anion transporter polypeptide-related protein 4) (oatp-rp4) (oatprp4). [swissprot;acc:q9h2y9]
5034	rap1 gtpase-gdp dissociation stimulator 1 (smg p21 stimulatory gdp/gtp exchange protein) (smg gds protein) (exchange factor smggds). [swissprot;acc:p52306]
5033	signal recognition particle 14 kda protein (srp14) (18 kda alu rna binding protein). [swissprot;acc:p37108]
5032	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]
5031	cobw-like protein. [refseq;acc:nm_018491]
5030	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
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]
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]
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]
5026	tigger transposable element derived 6. [refseq;acc:nm_030953]
5025	thymidine kinase 2, mitochondrial precursor (ec 2.7.1.21) (mt-tk). [swissprot;acc:o00142]
5024	spinster-like protein. [sptrembl;acc:q9h2v7]
5023	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]
5022	histone deacetylase 3 (hd3) (rpd3-2). [swissprot;acc:o15379]
5021	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
5020	jerky protein homolog like (hhmjg). [swissprot;acc:q9y4a0]
5019	fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540]	8541.07	8539.89	1.00014
5018	rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175]	9420.7	9422.53	1.00019
5017	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	9334.3	9331.78	1.00027
5016	inad-like protein isoform 3; pdz domain protein (drosophila inad-like); protein associated to tight junctions; pals1-associated tight junction protein; inactivation no after-potential d-like protein. [refseq;acc:nm_005799]	9417.53	9420.15	1.00028
5015	multiple pdz domain protein. [refseq;acc:nm_003829]	9417.11	9419.83	1.00029
5014	elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127]	9416.83	9419.63	1.0003
5013	ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312]
5012	rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756]	9412.17	9416.13	1.00042

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.