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 Hugo 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  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
red
green
network_comparison
1280 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] CYP4A11 218.368 213.22 1.02414
1281 cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] CYP4F3
1282 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] CYP4F8
1283 likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] CYP4X1
1284 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] CYP4F12
1285 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] CYP4F2
1286 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] CYP4F11
1287 dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] CYP4A22
1288 cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] CYP4B1
1289 flotillin-1. [swissprot;acc:o75955] FLOT1
1290 sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] SESN1
1291 hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819] HAS2 221.093 226.399 1.024
1292 caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] CASP7 233.942 228.46
1293 apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [swissprot;acc:p42574] CASP3
1294 hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] HAS1 221.093 226.399
1295 hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219] HAS3
1296 glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] SLC37A1 209.062 204.174 1.02394
1297 proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] PRODH
1298 dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.12) (e2) (pdc-e2) (70 kda mitochondrial autoantigen of primary biliary cirrhosis) (pbc) (m2 antigen complex 70 kda subunit). [swissprot;acc:p10515] DLAT 206.482 211.404 1.02384
1299 mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] PMPCB 217.635 212.575 1.0238
1300 mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] PMPCA 217.634 212.576 1.02379
1301 tumor protein d54 (hd54) (d52-like 2). [swissprot;acc:o43399] TPD52L2 206.852 211.757 1.02371
1302 ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] UQCRC1 217.624 212.584
1303 activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482] FHL5 269.157 275.531 1.02368
1304 glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [swissprot;acc:p00390] GSR 207.387 212.275 1.02357
1305 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] PPP3CA 218.439 213.436 1.02344
1306 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] PPP3CC 218.441 213.441 1.02343
1307 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] PPP3CB 218.44 213.44
1308 p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671] OCA2 213.439
1309 prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] VBP1 226.439 221.26 1.02341
1310 prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] PFDN2
1311 uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] UXT
1312 rad50 homolog isoform 1. [refseq;acc:nm_005732] RAD50 199.739 204.407 1.02337
1313 signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763] STAT3 222.573 227.75 1.02326
1314 signal transducer and activator of transcription 4. [swissprot;acc:q14765] STAT4 227.751
1315 signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224] STAT1 222.574 227.752
1316 signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226] STAT6 222.569 227.739 1.02323
1317 centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] CENPJ 206.773 202.105 1.0231
1318 signal transducer and activator of transcription 5a. [swissprot;acc:p42229] STAT5A 222.546 227.673 1.02304
1319 glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] GYS1 159.75 156.153
1320 signal transducer and activator of transcription 5b. [swissprot;acc:p51692] STAT5B 222.544 227.667 1.02302
1321 probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] DIMT1L 226.347 221.259 1.023
1322 endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] no value 159.86 156.275 1.02294
1323 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] NCK2 205.225 200.625 1.02293
1324 glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] GYS2 159.993 156.421 1.02284
1325 werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] WRNIP1 217.133 212.289 1.02282
1326 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] CSMD1 218.509 213.648 1.02275
1327 zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1] ZIC4
1328 calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [swissprot;acc:q14206] RCAN2 213.649
1329 dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] no value 213.648

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/