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 1280 to 1329 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1280	dehydrodolichyl diphosphate synthase. [source:refseq;acc:nm_024887]	6350.81	6874.88	1.08252	
1281	orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [source: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). [source:swissprot;acc:q92570]	6230.38	6744.35	1.08249	
1283	orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [source:swissprot;acc:p43354]	6229.16	6742.79	1.08246	
1284	xenotropic and polytropic retrovirus receptor. [source:refseq;acc:nm_004736]	6413.32	6941.48	1.08235	
1285	cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [source: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). [source: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). [source:swissprot;acc:q08477]	5655.85	6120.64	1.08218	
1288	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [source:swissprot;acc:p98187]	5655.85	6120.64	1.08218	
1289	likely ortholog of rat cytochrome p450 4x1. [source:refseq;acc:nm_178033]	5655.85	6120.64	1.08218	
1290	cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [source:swissprot;acc:q9hcs2]	5655.85	6120.64	1.08218	
1291	cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [source:swissprot;acc:p78329]	5655.85	6120.64	1.08218	
1292	cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [source:swissprot;acc:q9hbi6]	5655.85	6120.64	1.08218	
1293	dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [source:sptrembl;acc:q9ntl5]	5655.85	6120.64	1.08218	
1294	sestrin 3. [source:swissprot;acc:p58005]	5655.85	6120.65	1.08218	
1295	cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [source:swissprot;acc:p13584]	5655.85	6120.64	1.08218	
1296	flotillin-1. [source:swissprot;acc:o75955]	5655.85	6120.64	1.08218	
1297	sestrin 2 (hi95). [source:swissprot;acc:p58004]	5655.85	6120.65	1.08218	
1298	sestrin 1 (p53-regulated protein pa26). [source:swissprot;acc:q9y6p5]	5655.85	6120.62	1.08218	
1299	cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [source:swissprot;acc:q15070]	5589.33	6047.9	1.08204	
1300	60s ribosomal protein l34, mitochondrial precursor (l34mt). [source:swissprot;acc:q9bq48]	5589.33	6047.9	1.08204	
1301	electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [source: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). [source:swissprot;acc:q13162]	6343.26	6862.94	1.08193	
1303	cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [source:refseq;acc:nm_016441]	6334.15	6852.61	1.08185	
1304	fibulin-1 precursor. [source:swissprot;acc:p23142]	8550.79	9248.06	1.08154	
1305	glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [source:swissprot;acc:p47897]	5500.92	5949.26	1.0815	
1306	spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [source:swissprot;acc:p19623]	5500.92	5949.26	1.0815	
1307	glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [source:swissprot;acc:p41250]	5500.92	5949.26	1.0815	
1308	glutamyl trna synthetase. [source:sptrembl;acc:o14563]	5500.92	5949.26	1.0815	
1309	protein ad-016 (protein cgi-116) (x0009). [source:swissprot;acc:q9y3c0]	6110.09	6607.81	1.08146	
1310	mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [source:swissprot;acc:q15750]	6051.23	6544.17	1.08146	
1311	exocyst complex component sec8. [source:swissprot;acc:q96a65]	6221.22	6727.77	1.08142	
1312	u2 small nuclear ribonucleoprotein b". [source: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). [source:swissprot;acc:p10809]	5457.14	5899.85	1.08112	
1314	vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [source:swissprot;acc:q9nrw7]	5401.39	5838.63	1.08095	
1315	dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [source:swissprot;acc:p54098]	5685.77	6145.43	1.08084	
1316	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [source:swissprot;acc:q9y466]	6105.93	6599.41	1.08082	
1317	orphan nuclear receptor tr2. [source:swissprot;acc:p13056]	6105.69	6599.06	1.0808	
1318	serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [source:swissprot;acc:q96py6]	5961.97	6443.07	1.08069	
1319	serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [source:swissprot;acc:p51956]	5961.97	6443.07	1.08069	
1320	glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [source:swissprot;acc:p04406]	5961.97	6443.07	1.08069	
1321	suppressor of var1, 3-like 1. [source:refseq;acc:nm_003171]	6439.79	6959.21	1.08066	
1322	bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [source:swissprot;acc:q99933]	6439.79	6959.21	1.08066	
1323	glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [source:swissprot;acc:p49840]	6439.79	6959.21	1.08066	
1324	glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [source:swissprot;acc:p49841]	6439.79	6959.21	1.08066	
1325	serine/threonine protein phosphatase 2b catalytic subunit, alpha isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, alpha isoform) (cam-prp catalytic subunit). [source:swissprot;acc:q08209]	5656.79	6112.02	1.08047	
1326	mitochondrial gtp binding protein isoform v. [source:refseq;acc:nm_032620]	6222.8	6723.54	1.08047	
1327	p protein (melanocyte-specific transporter protein). [source:swissprot;acc:q04671]	5656.8	6111.9	1.08045	
1328	serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [source:swissprot;acc:p16299]	5656.81	6111.84	1.08044	
1329	serine/threonine protein phosphatase 2b catalytic subunit, gamma isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, gamma isoform) (calcineurin, testis-specific catalytic subunit) (cam-prp catalytic subunit). [source:swissprot;acc:p48454]	5656.82	6111.8	1.08043	

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/