Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

Results: HTML CSV LaTeX

Showing element 2513 to 2562 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
315	arginyl-trna synthetase-like; arginine-trna ligase. [source:refseq;acc:nm_020320]	Squared	Subtracted	31819.7	39222.2	7402.5	
315	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [source:swissprot;acc:q05329]	Rooted	Subtracted	59.6399	51.9242	7.7157	
315	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	Ranked	Subtracted	88.2482	110.265	22.0168	
315	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [source:swissprot;acc:p50579]	Ranked	Divided	244.126	268.604	1.10027	
315	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [source:swissprot;acc:p12882]	Rooted	Divided	95.0526	85.3206	1.11406	
315	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [source:swissprot;acc:q92824]	Squared	Divided	71576.8	56326.7	1.27074	
315	ribosome biogenesis regulatory protein homolog. [source:swissprot;acc:q15050]	Measured	Divided	21370.8	17896.5	1.19413	
315	vav proto-oncogene. [source:swissprot;acc:p15498]	Measured	Subtracted	6644.99	7707.8	1062.81	
316	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [source:swissprot;acc:q99747]	Rooted	Subtracted	59.6399	51.9242	7.7157	
316	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	Ranked	Subtracted	88.2482	110.265	22.0168	
316	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [source:swissprot;acc:p12883]	Rooted	Divided	95.0526	85.3206	1.11406	
316	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	Squared	Divided	28918.3	36746	1.27068	
316	protein translation factor sui1 homolog (sui1iso1). [source:swissprot;acc:p41567]	Ranked	Divided	242.694	267.017	1.10022	
316	regulator of chromosome condensation (cell cycle regulatory protein). [source:swissprot;acc:p18754]	Squared	Subtracted	44848.2	52108.3	7260.1	
316	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [source:swissprot;acc:p08129]	Measured	Divided	21370.8	17896.5	1.19413	
316	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [source:swissprot;acc:o43516]	Measured	Subtracted	6603.41	7664.65	1061.24	
317	adiponectin receptor 2. [source:refseq;acc:nm_024551]	Measured	Divided	3153.1	3762.56	1.19329	
317	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [source:sptrembl;acc:q9h430]	Rooted	Divided	95.0526	85.3206	1.11406	
317	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [source:swissprot;acc:q99259]	Rooted	Subtracted	59.6399	51.9242	7.7157	
317	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]	Ranked	Subtracted	88.2482	110.265	22.0168	
317	nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [source:swissprot;acc:q13232]	Squared	Divided	33982.3	43159.1	1.27005	
317	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [source:swissprot;acc:q15393]	Ranked	Divided	224.445	204.044	1.09998	
317	vav-3 protein. [source:swissprot;acc:q9ukw4]	Measured	Subtracted	6647.43	7706.18	1058.75	
317	zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [source:swissprot;acc:o60315]	Squared	Subtracted	44848.2	52108.3	7260.1	
318	1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [source:swissprot;acc:q9nrz7]	Measured	Subtracted	7485.08	8543.66	1058.58	
318	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [source:swissprot;acc:q9nrg0]	Rooted	Subtracted	38.8223	46.4975	7.6752	
318	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	Ranked	Subtracted	88.2482	110.265	22.0168	
318	mitochondrial 60s ribosomal protein l3 (l3mt). [source:swissprot;acc:p09001]	Ranked	Divided	242.011	266.18	1.09987	
318	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [source:swissprot;acc:q15388]	Squared	Divided	46739.9	59134.5	1.26518	
318	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	Rooted	Divided	95.0526	85.3206	1.11406	
318	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	Measured	Divided	34190.9	40795.8	1.19318	
318	transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [source:swissprot;acc:p37275]	Squared	Subtracted	44848.2	52108.3	7260.1	
319	1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [source:swissprot;acc:q9nrz5]	Measured	Subtracted	7477	8532.02	1055.02	
319	60s ribosomal protein l19. [source:swissprot;acc:p14118]	Ranked	Divided	240.73	264.729	1.09969	
319	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [source:refseq;acc:nm_015681]	Rooted	Subtracted	53.4993	45.9227	7.5766	
319	maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [source:swissprot;acc:q13368]	Squared	Subtracted	37147.5	44372.1	7224.6	
319	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]	Ranked	Subtracted	88.2482	110.265	22.0168	
319	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [source:swissprot;acc:p40855]	Squared	Divided	46739.9	59134.5	1.26518	
319	ras-related gtp binding a; ras-related gtp-binding protein. [source:refseq;acc:nm_006570]	Measured	Divided	20911	24908.5	1.19117	
319	saccharomyces cerevisiae nip7p homolog. [source:refseq;acc:nm_016101]	Rooted	Divided	49.0663	54.4978	1.1107	
320	40s ribosomal protein s29. [source:swissprot;acc:p30054]	Rooted	Divided	50.2784	45.294	1.11005	
320	carboxypeptidase b precursor. [source:refseq;acc:nm_020361]	Rooted	Subtracted	77.5801	70.0182	7.5619	
320	coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [source:swissprot;acc:p53621]	Squared	Subtracted	49280.5	42272.7	7007.8	
320	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [source:swissprot;acc:p12830]	Ranked	Divided	241.892	265.96	1.0995	
320	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [source:swissprot;acc:p07099]	Squared	Divided	87971.9	69563.1	1.26463	
320	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [source:swissprot;acc:q9unf1]	Ranked	Subtracted	88.2482	110.265	22.0168	
320	ras-related gtp binding c; rag c protein. [source:refseq;acc:nm_022157]	Measured	Divided	20911	24908.5	1.19117	
320	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [source:swissprot;acc:o95718]	Measured	Subtracted	10263.8	11318.6	1054.8	
321	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [source:sptrembl;acc:q9br02]	Ranked	Divided	241.892	265.959	1.09949	
321	fibulin-1 precursor. [source:swissprot;acc:p23142]	Squared	Subtracted	44407.1	51387.4	6980.3	

Legend:
- Rank is the rank after comparing the two networks
- 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.

- http://analysis.yellowcouch.org/