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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Value Type Rank Gene Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1280 to 1329 of 12912 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
red
green
network_comparison
1280 DHDDS dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887] 6350.81 6874.88 1.08252
1281 NR4A1 orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736] 6230.49 6744.5 1.0825
1282 NR4A3 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 NR4A2 orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [swissprot;acc:p43354] 6229.16 6742.79 1.08246
1284 XPR1 xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] 6413.32 6941.48 1.08235
1285 CNDP2 cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4] 6207.57 6718.7 1.08234
1286 CYP4A11 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 CYP4F3 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 CYP4F8 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]
1289 CYP4X1 likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033]
1290 CYP4F12 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2]
1291 CYP4F2 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 CYP4F11 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6]
1293 CYP4A22 dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5]
1294 SESN3 sestrin 3. [swissprot;acc:p58005] 6120.65
1295 CYP4B1 cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] 6120.64
1296 FLOT1 flotillin-1. [swissprot;acc:o75955]
1297 SESN2 sestrin 2 (hi95). [swissprot;acc:p58004] 6120.65
1298 SESN1 sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] 6120.62
1299 OXA1L cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] 5589.33 6047.9 1.08204
1300 MRPL34 60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48]
1301 ETFDH 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 PRDX4 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 CRIM1 cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441] 6334.15 6852.61 1.08185
1304 FBLN1 fibulin-1 precursor. [swissprot;acc:p23142] 8550.79 9248.06 1.08154
1305 QARS glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] 5500.92 5949.26 1.0815
1306 SRM spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623]
1307 GARS glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250]
1308 EARS2 glutamyl trna synthetase. [sptrembl;acc:o14563]
1309 CCDC53 protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] 6110.09 6607.81 1.08146
1310 MAP3K7IP1 mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750] 6051.23 6544.17
1311 EXOC4 exocyst complex component sec8. [swissprot;acc:q96a65] 6221.22 6727.77 1.08142
1312 SNRPB2 u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] 5675.96 6136.47 1.08113
1313 HSPD1 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
1314 VPS45 vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7] 5401.39 5838.63 1.08095
1315 POLG dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] 5685.77 6145.43 1.08084
1316 NR2E1 orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] 6105.93 6599.41 1.08082
1317 NR2C1 orphan nuclear receptor tr2. [swissprot;acc:p13056] 6105.69 6599.06 1.0808
1318 NEK1 serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] 5961.97 6443.07 1.08069
1319 NEK3 serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [swissprot;acc:p51956]
1320 GAPDH glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406]
1321 SUPV3L1 suppressor of var1, 3-like 1. [refseq;acc:nm_003171] 6439.79 6959.21 1.08066
1322 BAG1 bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933]
1323 GSK3A glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840]
1324 GSK3B glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841]
1325 PPP3CA 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). [swissprot;acc:q08209] 5656.79 6112.02 1.08047
1326 GTPBP3 mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] 6222.8 6723.54
1327 OCA2 p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671] 5656.8 6111.9 1.08045
1328 PPP3CB 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). [swissprot;acc:p16299] 5656.81 6111.84 1.08044
1329 PPP3CC 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). [swissprot;acc:p48454] 5656.82 6111.8 1.08043

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
- Hugo is the HGNC identifier if it exists
- 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/