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 1382 to 1431 of 3228 in total

Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1382	histidine ammonia-lyase (ec 4.3.1.3) (histidase). [source:swissprot;acc:p42357]	6079.46	6555.41	1.07829	
1383	ribosomal protein s6 kinase alpha 6 (ec 2.7.1.37) (s6k-alpha 6) (90 kda ribosomal protein s6 kinase 6) (p90-rsk 6) (ribosomal s6 kinase 4) (rsk-4) (pp90rsk4). [source:swissprot;acc:q9uk32]	6079.45	6555.4	1.07829	
1384	ribosomal protein s6 kinase alpha 2 (ec 2.7.1.37) (s6k-alpha 2) (90 kda ribosomal protein s6 kinase 2) (p90-rsk 2) (ribosomal s6 kinase 3) (rsk-3) (pp90rsk3). [source:swissprot;acc:q15349]	6079.45	6555.4	1.07829	
1385	calcium/calmodulin-dependent protein kinase type ii alpha chain (ec 2.7.1.123) (cam-kinase ii alpha chain) (cam kinase ii alpha subunit) (camk-ii alpha subunit). [source:swissprot;acc:q9uqm7]	6079.45	6555.4	1.07829	
1386	calcium/calmodulin-dependent protein kinase type ii beta chain (ec 2.7.1.123) (cam-kinase ii beta chain) (cam kinase ii beta subunit) (camk-ii beta subunit). [source:swissprot;acc:q13554]	6079.46	6555.41	1.07829	
1387	mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [source:swissprot;acc:q99683]	6079.46	6555.4	1.07829	
1388	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]	5743.39	6192.94	1.07827	
1389	mitogen-activated protein kinase 1 (ec 2.7.1.37) (extracellular signal-regulated kinase 2) (erk-2) (mitogen-activated protein kinase 2) (map kinase 2) (mapk 2) (p42-mapk) (ert1). [source:swissprot;acc:p28482]	6079.13	6554.85	1.07825	
1390	receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [source:swissprot;acc:q15303]	5743.36	6192.72	1.07824	
1391	epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [source:swissprot;acc:p00533]	5743.36	6192.7	1.07824	
1392	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]	5743.36	6192.7	1.07824	
1393	2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [source:swissprot;acc:q9uj83]	5743.36	6192.72	1.07824	
1394	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]	5743.36	6192.72	1.07824	
1395	lin-7 homolog c; lin-7 protein 3. [source:refseq;acc:nm_018362]	5743.26	6191.96	1.07813	
1396	g-rich sequence factor-1 (grsf-1). [source:swissprot;acc:q12849]	5803.54	6256.54	1.07806	
1397	heterogeneous nuclear ribonucleoprotein f (hnrnp f). [source:swissprot;acc:p52597]	5803.27	6256.23	1.07805	
1398	heterogeneous nuclear ribonucleoprotein h (hnrnp h). [source:swissprot;acc:p31943]	5803.12	6256.05	1.07805	
1399	heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [source:swissprot;acc:p55795]	5803.1	6256.03	1.07805	
1400	heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [source:swissprot;acc:p31942]	5803.45	6256.43	1.07805	
1401	hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [source:swissprot;acc:p55318]	5728.92	6175.99	1.07804	
1402	43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [source:swissprot;acc:q13702]	6160.06	6640.78	1.07804	
1403	importin 4. [source:refseq;acc:nm_024658]	5613.16	6050.16	1.07785	
1404	mesoderm induction early response 1. [source:refseq;acc:nm_020948]	6291.89	6781.6	1.07783	
1405	proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [source:swissprot;acc:p25788]	6291.89	6781.6	1.07783	
1406	ribokinase (ec 2.7.1.15). [source:swissprot;acc:q9h477]	6210.51	6693.49	1.07777	
1407	transketolase (ec 2.2.1.1) (tk). [source:swissprot;acc:p29401]	5692.53	6134.64	1.07766	
1408	serologically defined colon cancer antigen 16. [source:refseq;acc:nm_006649]	6268.94	6755.57	1.07763	
1409	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (ec 2.6.1.16) (hexosephosphate aminotransferase 2) (d-fructose-6- phosphate amidotransferase 2) (gfat 2) (gfat2). [source:swissprot;acc:o94808]	5358.19	5773.37	1.07749	
1410	delta-interacting protein a (hepatitis delta antigen interacting protein a). [source:swissprot;acc:q15834]	6274.62	6760.78	1.07748	
1411	14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [source:swissprot;acc:p31946]	5812.02	6262.07	1.07743	
1412	histone deacetylase 5 (hd5) (antigen ny-co-9). [source:swissprot;acc:q9uql6]	5813.84	6263.92	1.07742	
1413	histone deacetylase 9 (hd9) (hd7b) (hd7). [source:swissprot;acc:q9ukv0]	5813.88	6263.97	1.07742	
1414	histone deacetylase 4 (hd4). [source:swissprot;acc:p56524]	5813.88	6263.96	1.07741	
1415	14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [source:swissprot;acc:p29312]	5815.33	6265.44	1.0774	
1416	xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [source:refseq;acc:nm_020385]	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]	5360.39	5775.24	1.07739	
1418	isocitrate dehydrogenase [nad] subunit beta, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [source:swissprot;acc:o43837]	5360.39	5775.24	1.07739	
1419	isocitrate dehydrogenase [nad] subunit gamma, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [source:swissprot;acc:p51553]	5360.39	5775.24	1.07739	
1420	zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [source:swissprot;acc:q15915]	5658.51	6096.21	1.07735	
1421	importin 7; ran-binding protein 7. [source:refseq;acc:nm_006391]	5628.53	6063.61	1.0773	
1422	importin 8; ran-binding protein 8. [source:refseq;acc:nm_006390]	5628.53	6063.61	1.0773	
1423	brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [source:swissprot;acc:q9y6d5]	5628.53	6063.61	1.0773	
1424	hsgcn1 (fragment). [source:sptrembl;acc:q99736]	5628.53	6063.61	1.0773	
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]	5628.53	6063.61	1.0773	
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]	5362.85	5777.33	1.07729	
1427	zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [source:swissprot;acc:o60481]	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]	5880.37	6334.71	1.07726	
1429	similar to kinase suppressor of ras (fragment). [source:sptrembl;acc:q8ivt5]	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]	5880.37	6334.71	1.07726	
1431	limkain beta 2. [source:refseq;acc:nm_025140]	5796.03	6243.78	1.07725	

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/