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

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Showing element 1375 to 1424 of 3228 in total

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

Rank	description	red	green	network_comparison
1375	calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [swissprot;acc:q13555]	6079.45	6555.4	1.07829
1376	calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [swissprot;acc:q13557]	6079.46	6555.41
1377	mitogen-activated protein kinase kinase kinase 6 (ec 2.7.1.-). [swissprot;acc:o95382]		6555.4
1378	signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556]	6079.45
1379	ribosomal protein s6 kinase alpha 1 (ec 2.7.1.37) (s6k-alpha 1) (90 kda ribosomal protein s6 kinase 1) (p90-rsk 1) (ribosomal s6 kinase 1) (rsk-1) (pp90rsk1). [swissprot;acc:q15418]	6079.46	6555.41
1380	atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288]
1381	glutaryl-coa dehydrogenase, mitochondrial precursor (ec 1.3.99.7) (gcd). [swissprot;acc:q92947]
1382	histidine ammonia-lyase (ec 4.3.1.3) (histidase). [swissprot;acc:p42357]
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). [swissprot;acc:q9uk32]	6079.45	6555.4
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). [swissprot;acc:q15349]
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). [swissprot;acc:q9uqm7]
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). [swissprot;acc:q13554]	6079.46	6555.41
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). [swissprot;acc:q99683]		6555.4
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). [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). [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). [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). [swissprot;acc:p00533]		6192.7
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). [swissprot;acc:p04626]
1393	2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83]		6192.72
1394	receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860]
1395	lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362]	5743.26	6191.96	1.07813
1396	g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849]	5803.54	6256.54	1.07806
1397	heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597]	5803.27	6256.23	1.07805
1398	heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943]	5803.12	6256.05
1399	heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795]	5803.1	6256.03
1400	heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942]	5803.45	6256.43
1401	hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [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). [swissprot;acc:q13702]	6160.06	6640.78
1403	importin 4. [refseq;acc:nm_024658]	5613.16	6050.16	1.07785
1404	mesoderm induction early response 1. [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). [swissprot;acc:p25788]
1406	ribokinase (ec 2.7.1.15). [swissprot;acc:q9h477]	6210.51	6693.49	1.07777
1407	transketolase (ec 2.2.1.1) (tk). [swissprot;acc:p29401]	5692.53	6134.64	1.07766
1408	serologically defined colon cancer antigen 16. [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). [swissprot;acc:o94808]	5358.19	5773.37	1.07749
1410	delta-interacting protein a (hepatitis delta antigen interacting protein a). [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). [swissprot;acc:p31946]	5812.02	6262.07	1.07743
1412	histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6]	5813.84	6263.92	1.07742
1413	histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0]	5813.88	6263.97
1414	histone deacetylase 4 (hd4). [swissprot;acc:p56524]		6263.96	1.07741
1415	14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312]	5815.33	6265.44	1.0774
1416	xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385]	6123.75	6597.71
1417	isocitrate dehydrogenase [nad] subunit alpha, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [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). [swissprot;acc:o43837]
1419	isocitrate dehydrogenase [nad] subunit gamma, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p51553]
1420	zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915]	5658.51	6096.21	1.07735
1421	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	5628.53	6063.61	1.0773
1422	importin 8; ran-binding protein 8. [refseq;acc:nm_006390]
1423	brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5]
1424	hsgcn1 (fragment). [sptrembl;acc:q99736]

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.