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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 2830 to 2879 of 6456 in total 
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1415	caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [source:swissprot;acc:p55210]	Subtracted	4633.48	5084.24	450.76	
1416	apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [source:swissprot;acc:p42574]	Subtracted	4633.48	5084.24	450.76	
1416	xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [source:refseq;acc:nm_020385]	Divided	6123.75	6597.71	1.0774	
1417	isocitrate dehydrogenase [nad] subunit alpha, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [source:swissprot;acc:p50213]	Divided	5360.39	5775.24	1.07739	
1417	p53-related protein kinase (ec 2.7.1.-) (nori-2). [source:swissprot;acc:q96s44]	Subtracted	5346.11	5796.72	450.61	
1418	14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [source:swissprot;acc:p29312]	Subtracted	5815.33	6265.44	450.11	
1418	isocitrate dehydrogenase [nad] subunit beta, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [source:swissprot;acc:o43837]	Divided	5360.39	5775.24	1.07739	
1419	histone deacetylase 9 (hd9) (hd7b) (hd7). [source:swissprot;acc:q9ukv0]	Subtracted	5813.88	6263.97	450.09	
1419	isocitrate dehydrogenase [nad] subunit gamma, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [source:swissprot;acc:p51553]	Divided	5360.39	5775.24	1.07739	
1420	histone deacetylase 5 (hd5) (antigen ny-co-9). [source:swissprot;acc:q9uql6]	Subtracted	5813.84	6263.92	450.08	
1420	zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [source:swissprot;acc:q15915]	Divided	5658.51	6096.21	1.07735	
1421	histone deacetylase 4 (hd4). [source:swissprot;acc:p56524]	Subtracted	5813.88	6263.96	450.08	
1421	importin 7; ran-binding protein 7. [source:refseq;acc:nm_006391]	Divided	5628.53	6063.61	1.0773	
1422	14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [source:swissprot;acc:p31946]	Subtracted	5812.02	6262.07	450.05	
1422	importin 8; ran-binding protein 8. [source:refseq;acc:nm_006390]	Divided	5628.53	6063.61	1.0773	
1423	brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [source:swissprot;acc:q9y6d5]	Divided	5628.53	6063.61	1.0773	
1423	lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [source:refseq;acc:nm_004664]	Subtracted	5743.45	6193.45	450	
1424	hsgcn1 (fragment). [source:sptrembl;acc:q99736]	Divided	5628.53	6063.61	1.0773	
1424	lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [source:refseq;acc:nm_022165]	Subtracted	5743.39	6192.94	449.55	
1425	brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [source:swissprot;acc:q9y6d6]	Divided	5628.53	6063.61	1.0773	
1425	receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [source:swissprot;acc:q15303]	Subtracted	5743.36	6192.72	449.36	
1426	2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [source:swissprot;acc:q9uj83]	Subtracted	5743.36	6192.72	449.36	
1426	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [source:swissprot;acc:q06210]	Divided	5362.85	5777.33	1.07729	
1427	receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [source:swissprot;acc:p21860]	Subtracted	5743.36	6192.72	449.36	
1427	zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [source:swissprot;acc:o60481]	Divided	5658.55	6095.85	1.07728	
1428	dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [source:swissprot;acc:q02750]	Divided	5880.37	6334.71	1.07726	
1428	epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [source:swissprot;acc:p00533]	Subtracted	5743.36	6192.7	449.34	
1429	receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [source:swissprot;acc:p04626]	Subtracted	5743.36	6192.7	449.34	
1429	similar to kinase suppressor of ras (fragment). [source:sptrembl;acc:q8ivt5]	Divided	5880.37	6334.71	1.07726	
1430	dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [source:swissprot;acc:p36507]	Divided	5880.37	6334.71	1.07726	
1430	transducin beta-like 3; wd-repeat protein sazd. [source:refseq;acc:nm_006453]	Subtracted	4025.3	4474.3	449	
1431	limkain beta 2. [source:refseq;acc:nm_025140]	Divided	5796.03	6243.78	1.07725	
1431	lin-7 homolog c; lin-7 protein 3. [source:refseq;acc:nm_018362]	Subtracted	5743.26	6191.96	448.7	
1432	glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [source:swissprot;acc:p47897]	Subtracted	5500.92	5949.26	448.34	
1432	zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [source:swissprot;acc:o95409]	Divided	5658.58	6095.62	1.07723	
1433	dna topoisomerase iii alpha (ec 5.99.1.2). [source:swissprot;acc:q13472]	Divided	5692.34	6131.71	1.07719	
1433	spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [source:swissprot;acc:p19623]	Subtracted	5500.92	5949.26	448.34	
1434	glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [source:swissprot;acc:p41250]	Subtracted	5500.92	5949.26	448.34	
1434	myosin viia. [source:swissprot;acc:q13402]	Divided	5759.68	6203.63	1.07708	
1435	glutamyl trna synthetase. [source:sptrembl;acc:o14563]	Subtracted	5500.92	5949.26	448.34	
1435	ubiquitin-conjugating enzyme e2 b (ec 6.3.2.19) (ubiquitin-protein ligase b) (ubiquitin carrier protein b) (hr6b) (hhr6b) (e2-17 kda). [source:swissprot;acc:p23567]	Divided	5759.68	6203.63	1.07708	
1436	casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [source:swissprot;acc:p19138]	Subtracted	4307.12	4755.03	447.91	
1436	ubiquitin-conjugating enzyme e2 a (ec 6.3.2.19) (ubiquitin-protein ligase a) (ubiquitin carrier protein a) (hr6a) (hhr6a). [source:swissprot;acc:p49459]	Divided	5759.68	6203.63	1.07708	
1437	casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [source:swissprot;acc:p19784]	Subtracted	4307.12	4755.03	447.91	
1437	glycerol-3-phosphate dehydrogenase, mitochondrial precursor (ec 1.1.99.5) (gpd-m) (gpdh-m). [source:swissprot;acc:p43304]	Divided	6089.43	6558.02	1.07695	
1438	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [source:refseq;acc:nm_015681]	Subtracted	3886.62	3438.82	447.8	
1438	exocyst complex component sec10 (hsec10). [source:swissprot;acc:o00471]	Divided	6721.25	7238.34	1.07693	
1439	camp response element-binding protein cre-bpa. [source:refseq;acc:nm_004904]	Divided	5658.8	6093.56	1.07683	
1439	limkain beta 2. [source:refseq;acc:nm_025140]	Subtracted	5796.03	6243.78	447.75	
1440	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [source:swissprot;acc:p45954]	Subtracted	6296.52	6743.85	447.33	

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/