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	network_comparison	red	Interaction Map	Gene	Network Comparison Type	Rank	description

Results: HTML CSV LaTeX

Showing element 501 to 550 of 2121 in total

network_comparison  : 0
Network Comparison Type  : Subtracted

Value Type	Filtered	green	red	Interaction Map	Rank	description
Measured	1	0	0	Low confidence	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	0			High confidence	501	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
					502	brca1 associated protein. [refseq;acc:nm_006768]
				Low confidence	837	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
					838	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
					839	cobw-like protein. [refseq;acc:nm_018491]
					841	gamma-glutamyltransferase. [sptrembl;acc:q14390]
					842	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
					843	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
		394	394	High confidence	500	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]
				Low confidence	840
	1	0	0	High confidence	2756	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]
					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.