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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank Gene Hugo description Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1301 to 1350 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		network_comparison
    		green
    1301 TPD52L2 tumor protein d54 (hd54) (d52-like 2). [swissprot;acc:o43399] 206.852 1.02371 211.757
    1302 UQCRC1 ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] 217.624 212.584
    1303 FHL5 activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482] 269.157 1.02368 275.531
    1304 GSR glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [swissprot;acc:p00390] 207.387 1.02357 212.275
    1305 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] 218.439 1.02344 213.436
    1306 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] 218.441 1.02343 213.441
    1307 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] 218.44 213.44
    1308 OCA2 p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671] 213.439
    1309 VBP1 prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] 226.439 1.02341 221.26
    1310 PFDN2 prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9]
    1311 UXT uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9]
    1312 RAD50 rad50 homolog isoform 1. [refseq;acc:nm_005732] 199.739 1.02337 204.407
    1313 STAT3 signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763] 222.573 1.02326 227.75
    1314 STAT4 signal transducer and activator of transcription 4. [swissprot;acc:q14765] 227.751
    1315 STAT1 signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224] 222.574 227.752
    1316 STAT6 signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226] 222.569 1.02323 227.739
    1317 CENPJ centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] 206.773 1.0231 202.105
    1318 STAT5A signal transducer and activator of transcription 5a. [swissprot;acc:p42229] 222.546 1.02304 227.673
    1319 GYS1 glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] 159.75 156.153
    1320 STAT5B signal transducer and activator of transcription 5b. [swissprot;acc:p51692] 222.544 1.02302 227.667
    1321 DIMT1L probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] 226.347 1.023 221.259
    1322 no value endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] 159.86 1.02294 156.275
    1323 NCK2 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] 205.225 1.02293 200.625
    1324 GYS2 glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] 159.993 1.02284 156.421
    1325 WRNIP1 werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] 217.133 1.02282 212.289
    1326 CSMD1 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] 218.509 1.02275 213.648
    1327 ZIC4 zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1]
    1328 RCAN2 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] 213.649
    1329 no value dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] 213.648
    1330 RCAN1 calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] 218.508
    1331 RCAN3 calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8] 218.509 213.649
    1332 OXA1L cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] 220.681 1.02271 215.78
    1333 MRPL34 60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48]
    1334 PRAF2 jm4 protein. [refseq;acc:nm_007213] 199.643 1.02264 204.163
    1335 ARL6IP5 cytoskeleton related vitamin a responsive protein; glutamate transporter eeac1-associated protein; dermal papilla derived protein 11; putative mapk activating protein pm27. [refseq;acc:nm_006407] 199.771 1.02261 204.287
    1336 GALK2 n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] 215.162 1.02257 210.412
    1337 no value galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902]
    1338 GALE udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376]
    1339 NPC2 epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668] 205.204 1.02239 200.71
    1340 SUV39H2 histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [swissprot;acc:q9h5i1] 226.433 1.02234 231.491
    1341 EIF2S1 eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198]
    1342 SUV39H1 histone-lysine n-methyltransferase, h3 lysine-9 specific 1 (ec 2.1.1.43) (histone h3-k9 methyltransferase 1) (h3-k9-hmtase 1) (suppressor of variegation 3-9 homolog 1) (su(var)3-9 homolog 1). [swissprot;acc:o43463]
    1343 CDC25A m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] 258.558 1.02231 252.916
    1344 EXO1 exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027] 216.772 1.02224 221.594
    1345 FANCL phd finger protein 9. [refseq;acc:nm_018062]
    1346 SOLH small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632]
    1347 LIAS lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766] 204.961 1.02223 209.517
    1348 ZIC1 zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915] 218.569 1.02215 213.832
    1349 ZIC3 zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481] 218.572 1.02212 213.841
    1350 ZIC2 zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409] 218.574 1.0221 213.847

    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/