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.

Navigation/Query Panel:
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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1001 to 1050 of 16578 in total

Value Type  : Ranked
Filtered  : 1

green	Network Comparison Type	Rank	Interaction Map	description	network_comparison	red
0.00001	Divided	5031	Low confidence	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	1	0.00001
		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	High confidence	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	2.4	10
	Subtracted	537			14
28	Divided	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
		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]
	Subtracted	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
		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]
		582		cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]
28.4944	Divided	11	Low confidence	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	1.30966	37.318
	Subtracted	273			8.8236
28.5242	Divided	12		vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]	1.30933	37.3475
	Subtracted	274			8.8233
29.1831	Divided	13		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	1.30207	37.9984
		14		vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]
	Subtracted	277		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	8.8153
		278		vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]

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.