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

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Showing element 401 to 450 of 19268 in total

Value Type  : Ranked
Filtered  : 0
Network Comparison Type  : Divided

green	red	Rank	Interaction Map	network_comparison	description
10050.9	10347.7	627	Low confidence	1.02953	17-beta-hydroxysteroid dehydrogenase type vii-like. [refseq;acc:nm_182829]
10061.1	9997.58	796		1.00635	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]
10061.8	10449	382	High confidence	1.03848	actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]
10063.9	10372.1	617	Low confidence	1.03062	60s ribosomal protein l18a. [swissprot;acc:q02543]
10068.8	9414	460		1.06956	synaptotagmin xiv. [refseq;acc:nm_153262]
10095.3	10165.7	789		1.00697	seven in absentia homolog 1. [refseq;acc:nm_003031]
10111.2	9783.63	403	High confidence	1.03348	udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795]
		404			udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310]
		405			udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133]
		406			glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075]
		407			udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537]
		408			udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855]
10115	9339.12	393	Low confidence	1.08308	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765]
10137.2	10357.4	675		1.02172	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]
10148.1	9587.31	504		1.05849	ero1-like. [refseq;acc:nm_014584]
10165.2	11049.6	379		1.087	tubby protein homolog. [swissprot;acc:p50607]
10174.1	7704.7	69	High confidence	1.32051	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]
10199.8	10499.2	628	Low confidence	1.02935	trna selenocysteine associated protein. [refseq;acc:nm_017846]
10201.4	9854.67	392	High confidence	1.03518	seven in absentia homolog 1. [refseq;acc:nm_003031]
10203.5	10381.1	712	Low confidence	1.01741	rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427]
10228.3	8335.82	96	High confidence	1.22703	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]
		97			microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]
10231.3	11573.8	182		1.13121	putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544]
10243.1	10156.4	478		1.00854	3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110]
10248.3	10231.8	498		1.00161	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]
10251.3	10463.7	677	Low confidence	1.02072	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]
10251.6	11096.8	277	High confidence	1.08245	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]
10253.2	9966.23	631	Low confidence	1.02879	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]
10261.5	10028.5	434	High confidence	1.02323	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]
10277.3	9107.61	289	Low confidence	1.12843	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]
10278.1	9972.93	619		1.0306	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]
10320.9	9953.39	388	High confidence	1.03692	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521]
10324.5	13320.5	61	Low confidence	1.29018	protein kinase, lysine deficient 3. [refseq;acc:nm_020922]
10333	9929.99	584		1.04059	solute carrier family 35, member e2. [refseq;acc:nm_182838]
10338.7	10388.7	490	High confidence	1.00484	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]
10380	9630	408	Low confidence	1.07788	helicase/primase complex protein. [refseq;acc:nm_138336]
10391.6	9591.43	391		1.08343	dead-box protein. [refseq;acc:nm_018665]
10406.3	7853.67	65	High confidence	1.32502	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]
10410.1	11550.2	321	Low confidence	1.10952	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]
10412.4	11971.7	164	High confidence	1.14975	dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]
10432.9	9151.76	267	Low confidence	1.13999	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]
10433.9	10311.2	747		1.0119	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]
10437.1	12738.7	102	High confidence	1.22052	60s ribosomal protein l18a. [swissprot;acc:q02543]
10446.9	10316.6	739	Low confidence	1.01263	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]
10454.7	12787.8	99	High confidence	1.22316	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]
10466.5	9897.29	327		1.05751	3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]
10470.6	12584.5	110		1.20189	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]
10485.5	10736.2	653	Low confidence	1.02391	similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]
10489.3	12314.9	134	High confidence	1.17404	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]
		135			cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]

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.