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 2408 to 2457 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    2408 dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] no value 194.407 193.706 1.00362
    2409 lactoylglutathione lyase (ec 4.4.1.5) (methylglyoxalase) (aldoketomutase) (glyoxalase i) (glx i) (ketone-aldehyde mutase) (s-d-lactoylglutathione methylglyoxal lyase). [swissprot;acc:q04760] GLO1
    2410 lysophospholipase i; lysophospholipase 1; lysophospholipid-specific lysophospholipase; acyl-protein thioesterase-1. [refseq;acc:nm_006330] LYPLA1
    2411 mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] PBLD
    2412 lysophospholipase ii; acyl-protein thioesterase. [refseq;acc:nm_007260] LYPLA2P1
    2413 serpin b12. [swissprot;acc:q96p63] SERPINB12 218.2 218.984 1.00359
    2414 megsin (tp55) (serpin b7). [swissprot;acc:o75635] SERPINB7
    2415 hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] no value
    2416 oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [swissprot;acc:p55055] NR1H2
    2417 upf0183 protein. [swissprot;acc:q9bsu1] C16orf70
    2418 antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008] SERPINC1
    2419 translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q14232] EIF2B1
    2420 squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508] SERPINB4
    2421 apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797] AIFM2 210.205 209.454
    2422 oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133] NR1H3 218.2 218.984
    2423 histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6] HDAC5 220.682 221.471 1.00358
    2424 histone deacetylase 4 (hd4). [swissprot;acc:p56524] HDAC4 221.472
    2425 histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0] HDAC9
    2426 mesoderm induction early response 1. [refseq;acc:nm_020948] no value 212.374 211.618 1.00357
    2427 proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788] PSMA3
    2428 alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] no value 192.871 193.555 1.00355
    2429 esterase d (ec 3.1.1.1). [swissprot;acc:p10768] ESD
    2430 epsin 1; eh domain-binding mitotic phosphoprotein. [refseq;acc:nm_013333] EPN1 217.873 218.644 1.00354
    2431 proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787] PSMA2 213.048 212.3 1.00352
    2432 26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008] PSMD6 215.807 216.556 1.00347
    2433 elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] EEF1AL3 217.366 218.117 1.00346
    2434 methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] MTHFR 213.021 212.286
    2435 zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312] ZNF259 217.366 218.117
    2436 elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [swissprot;acc:q05639] EEF1A2
    2437 guanylate kinase (ec 2.7.4.8) (gmp kinase). [swissprot;acc:q16774] GUK1 219.361 220.116 1.00344
    2438 proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [swissprot;acc:p25789] PSMA4 214.049 213.323 1.0034
    2439 14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] YWHAB 220.681 221.425 1.00337
    2440 26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242] PSMD3 217.645 218.376 1.00336
    2441 electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] ETFA 180.137 180.732 1.0033
    2442 transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848] TAF6 204.419 203.748 1.00329
    2443 ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [swissprot;acc:p50550] UBE2I 217.073 216.364 1.00328
    2444 zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [swissprot;acc:q9hc78] ZBTB20 206.086 206.753 1.00324
    2445 kruppel-related zinc finger protein hckrox. [refseq;acc:nm_015872] ZBTB7B 206.088 206.756
    2446 epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] EPHX1 182.272 181.683
    2447 peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [swissprot;acc:o00628] PEX7 206.084 206.752
    2448 glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] no value 212.446 211.766 1.00321
    2449 phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674] CDS2 204.717 205.371 1.00319
    2450 proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072] PSMB6 213.85 213.177 1.00316
    2451 secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] SCAMP2 204.688 205.333 1.00315
    2452 secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] SCAMP3
    2453 secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] SCAMP1 205.332
    2454 solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] SLC13A4 204.683 205.326 1.00314
    2455 solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9] SLC13A3
    2456 solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2] SLC13A1
    2457 vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [swissprot;acc:p46459] NSF 213.588 212.92

    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/