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 description Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1301 to 1350 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    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
    1330 calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] RCAN1 218.508
    1331 calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8] RCAN3 218.509 213.649
    1332 cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] OXA1L 220.681 215.78 1.02271
    1333 60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48] MRPL34
    1334 jm4 protein. [refseq;acc:nm_007213] PRAF2 199.643 204.163 1.02264
    1335 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] ARL6IP5 199.771 204.287 1.02261
    1336 n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] GALK2 215.162 210.412 1.02257
    1337 galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] no value
    1338 udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] GALE
    1339 epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668] NPC2 205.204 200.71 1.02239
    1340 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] SUV39H2 226.433 231.491 1.02234
    1341 eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198] EIF2S1
    1342 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] SUV39H1
    1343 m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] CDC25A 258.558 252.916 1.02231
    1344 exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027] EXO1 216.772 221.594 1.02224
    1345 phd finger protein 9. [refseq;acc:nm_018062] FANCL
    1346 small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632] SOLH
    1347 lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766] LIAS 204.961 209.517 1.02223
    1348 zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915] ZIC1 218.569 213.832 1.02215
    1349 zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481] ZIC3 218.572 213.841 1.02212
    1350 zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409] ZIC2 218.574 213.847 1.0221

    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/