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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2300 to 2349 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    2300 ACAA1 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 191.563 192.541 1.00511
    2301 NMNAT3 nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] 217.392 218.498 1.00509
    2302 HMGCS2 hydroxymethylglutaryl-coa synthase, mitochondrial precursor (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:p54868] 191.567 192.542
    2303 HMGCR 3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035]
    2304 HMGCS1 hydroxymethylglutaryl-coa synthase, cytoplasmic (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:q01581]
    2305 ALDH18A1 delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [swissprot;acc:p54886] 217.392 218.498
    2306 ACAT1 acetyl-coa acetyltransferase, mitochondrial precursor (ec 2.3.1.9) (acetoacetyl-coa thiolase) (t2). [swissprot;acc:p24752] 191.571 192.544 1.00508
    2307 PRKAR2A camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] 215.554 214.467 1.00507
    2308 PRKX protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817] 215.543 214.459 1.00505
    2309 PRKACG camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 215.542
    2310 UBC ubiquitin. [swissprot;acc:p02248] 216.617 215.529
    2311 PRKACB camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694] 215.542 214.459
    2312 PRKACA camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612]
    2313 PRKAR2B camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] 215.529 214.449 1.00504
    2314 UBE2D2 ubiquitin-conjugating enzyme e2-17 kda 2 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 2). [swissprot;acc:p51669] 194.743 195.708 1.00496
    2315 ACACB acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763] 194.825 195.787 1.00494
    2316 no value 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] 217.241 218.311 1.00493
    2317 PPP6C serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] 194.834 195.794
    2318 SAPS3 sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312]
    2319 ACACA acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] 194.842 195.8 1.00492
    2320 RAD54L rad54-like protein; rad54 homolog. [refseq;acc:nm_003579] 219.292 218.218
    2321 no value tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] 203.909 202.925 1.00485
    2322 PDSS1 trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] 236.023 234.905 1.00476
    2323 NARS asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776] 192.773 193.691
    2324 PSMB1 proteasome subunit beta type 1 (ec 3.4.25.1) (proteasome component c5) (macropain subunit c5) (multicatalytic endopeptidase complex subunit c5) (proteasome gamma chain). [swissprot;acc:p20618] 212.129 211.129 1.00474
    2325 MTFMT methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] 221.728 220.685 1.00473
    2326 MAP2K4 dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] 220.076 219.05 1.00468
    2327 PSMC4 26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686] 217.413 218.426 1.00466
    2328 REXO4 xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] 209.326 208.357 1.00465
    2329 PSMD13 26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6] 217.112 218.116 1.00462
    2330 FARSB phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] 214.213 213.235 1.00459
    2331 MIZF mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] 229.258 230.294 1.00452
    2332 TMOD4 skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9]
    2333 TMOD3 ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]
    2334 TMOD1 tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289]
    2335 SNX9 sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]
    2336 TMOD2 neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1]
    2337 DLX2 homeobox protein dlx-2. [swissprot;acc:q07687]
    2338 DLX5 homeobox protein dlx-5. [swissprot;acc:p56178]
    2339 MPPED2 fetal brain protein 239 (239fb). [swissprot;acc:q15777]
    2340 DLX3 homeobox protein dlx-3. [swissprot;acc:o60479]
    2341 TNK2 activated p21cdc42hs kinase. [refseq;acc:nm_005781]
    2342 MAP3K7IP2 mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093]
    2343 no value glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] 212.222 211.27 1.00451
    2344 DAGLB kccr13l. [refseq;acc:nm_139179] 219.878 218.893 1.0045
    2345 RAD51 dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609]
    2346 NEK1 serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] 217.057 218.03 1.00448
    2347 NEK3 serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [swissprot;acc:p51956]
    2348 GAPDH glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406]
    2349 FBLN1 fibulin-1 precursor. [swissprot;acc:p23142] 192.348 191.503 1.00441

    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/