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 1264 to 1313 of 3228 in total

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

Rank	description	red	green	network_comparison
1264	cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941]	5894.47	6383.73	1.083
1265	dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135]
1266	sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691]
1267	cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850]
1268	sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137]
1269	xap-5 protein (hxc-26 protein). [swissprot;acc:q14320]
1270	epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [refseq;acc:nm_022772]	5685.08	6156.48	1.08292
1271	mitotic checkpoint serine/threonine-protein kinase bub1 beta (ec 2.7.1.-) (hbubr1) (mad3/bub1-related protein kinase) (mitotic checkpoint kinase mad3l). [swissprot;acc:o60566]	5528.65	5985.58	1.08265
1272	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]
1273	phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613]	5885	6371.14	1.08261
1274	3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405]
1275	3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213]
1276	peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77]	6437.99	6969.67	1.08258
1277	heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652]
1278	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]
1279	heat shock cognate 71 kda protein. [swissprot;acc:p11142]
1280	dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887]	6350.81	6874.88	1.08252
1281	orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736]	6230.49	6744.5	1.0825
1282	nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570]	6230.38	6744.35	1.08249
1283	orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [swissprot;acc:p43354]	6229.16	6742.79	1.08246
1284	xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736]	6413.32	6941.48	1.08235
1285	cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4]	6207.57	6718.7	1.08234
1286	cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928]	5655.85	6120.64	1.08218
1287	cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477]
1288	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]
1289	likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033]
1290	cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2]
1291	cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]
1292	cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6]
1293	dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5]
1294	sestrin 3. [swissprot;acc:p58005]		6120.65
1295	cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584]		6120.64
1296	flotillin-1. [swissprot;acc:o75955]
1297	sestrin 2 (hi95). [swissprot;acc:p58004]		6120.65
1298	sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5]		6120.62
1299	cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070]	5589.33	6047.9	1.08204
1300	60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48]
1301	electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134]	6618.74	7161.67	1.08203
1302	peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162]	6343.26	6862.94	1.08193
1303	cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441]	6334.15	6852.61	1.08185
1304	fibulin-1 precursor. [swissprot;acc:p23142]	8550.79	9248.06	1.08154
1305	glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897]	5500.92	5949.26	1.0815
1306	spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623]
1307	glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250]
1308	glutamyl trna synthetase. [sptrembl;acc:o14563]
1309	protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0]	6110.09	6607.81	1.08146
1310	mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750]	6051.23	6544.17
1311	exocyst complex component sec8. [swissprot;acc:q96a65]	6221.22	6727.77	1.08142
1312	u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579]	5675.96	6136.47	1.08113
1313	60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [swissprot;acc:p10809]	5457.14	5899.85	1.08112

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.