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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 3682 to 3731 of 19268 in total

Value Type  : Ranked
Filtered  : 1

green	Rank	description	Interaction Map	network_comparison	red	Network Comparison Type
0.00001	5022	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	Low confidence	1	0.00001	Divided
	5023	spinster-like protein. [sptrembl;acc:q9h2v7]
	5024	thymidine kinase 2, mitochondrial precursor (ec 2.7.1.21) (mt-tk). [swissprot;acc:o00142]
	5025	tigger transposable element derived 6. [refseq;acc:nm_030953]
	5026	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]
	5027	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]
	5028	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]
	5029	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
	5030	cobw-like protein. [refseq;acc:nm_018491]
	5031	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]
	5032	signal recognition particle 14 kda protein (srp14) (18 kda alu rna binding protein). [swissprot;acc:p37108]
	5033	rap1 gtpase-gdp dissociation stimulator 1 (smg p21 stimulatory gdp/gtp exchange protein) (smg gds protein) (exchange factor smggds). [swissprot;acc:p52306]
	5034	solute carrier family 21 member 15 (organic anion transporter polypeptide-related protein 4) (oatp-rp4) (oatprp4). [swissprot;acc:q9h2y9]
	5035	lipin 1. [swissprot;acc:q14693]
	5036	lipin 3 (lipin 3-like) (fragments). [swissprot;acc:q9bqk8]
	5037	myeloblast kiaa0230 (fragment). [sptrembl;acc:q92626]
	5038	testis specific leucine rich repeat protein. [refseq;acc:nm_012472]
	5039	major centromere autoantigen b (centromere protein b) (cenp-b). [swissprot;acc:p07199]
	5040	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]
	5041	n-acetylglucosamine kinase (ec 2.7.1.59) (glcnac kinase). [swissprot;acc:q9uj70]
	5042	transthyretin precursor (prealbumin) (tbpa) (ttr) (attr). [swissprot;acc:p02766]
	5043	late endosomal/lysosomal mp1 interacting protein (p14) (hspc003). [swissprot;acc:q9y2q5]
	5044	langerhans cell specific c-type lectin. [refseq;acc:nm_015717]
	5045	putative tumor suppressor 101f6. [refseq;acc:nm_007022]
	5046	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
	5047	double-stranded rna-binding zinc finger protein jaz. [refseq;acc:nm_012279]
	5048	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]
24	1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	High confidence	2.4	10
	537			14		Subtracted
28	2	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]		1.86667	15	Divided
	3	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]
	4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]
	5	cytohesin 4. [swissprot;acc:q9uia0]
	6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]
	578	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]		13		Subtracted
	579	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]
	580	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]
	581	cytohesin 4. [swissprot;acc:q9uia0]

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.