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 network_comparison green
    Results: HTML CSV LaTeX Showing element 2301 to 2350 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		network_comparison
    		green
    2301 nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] NMNAT3 217.392 1.00509 218.498
    2302 hydroxymethylglutaryl-coa synthase, mitochondrial precursor (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:p54868] HMGCS2 191.567 192.542
    2303 3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035] HMGCR
    2304 hydroxymethylglutaryl-coa synthase, cytoplasmic (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:q01581] HMGCS1
    2305 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] ALDH18A1 217.392 218.498
    2306 acetyl-coa acetyltransferase, mitochondrial precursor (ec 2.3.1.9) (acetoacetyl-coa thiolase) (t2). [swissprot;acc:p24752] ACAT1 191.571 1.00508 192.544
    2307 camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] PRKAR2A 215.554 1.00507 214.467
    2308 protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817] PRKX 215.543 1.00505 214.459
    2309 camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] PRKACG 215.542
    2310 ubiquitin. [swissprot;acc:p02248] UBC 216.617 215.529
    2311 camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694] PRKACB 215.542 214.459
    2312 camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612] PRKACA
    2313 camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] PRKAR2B 215.529 1.00504 214.449
    2314 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] UBE2D2 194.743 1.00496 195.708
    2315 acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763] ACACB 194.825 1.00494 195.787
    2316 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] no value 217.241 1.00493 218.311
    2317 serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] PPP6C 194.834 195.794
    2318 sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] SAPS3
    2319 acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] ACACA 194.842 1.00492 195.8
    2320 rad54-like protein; rad54 homolog. [refseq;acc:nm_003579] RAD54L 219.292 218.218
    2321 tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] no value 203.909 1.00485 202.925
    2322 trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] PDSS1 236.023 1.00476 234.905
    2323 asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776] NARS 192.773 193.691
    2324 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] PSMB1 212.129 1.00474 211.129
    2325 methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] MTFMT 221.728 1.00473 220.685
    2326 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] MAP2K4 220.076 1.00468 219.05
    2327 26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686] PSMC4 217.413 1.00466 218.426
    2328 xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] REXO4 209.326 1.00465 208.357
    2329 26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6] PSMD13 217.112 1.00462 218.116
    2330 phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] FARSB 214.213 1.00459 213.235
    2331 mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] MIZF 229.258 1.00452 230.294
    2332 skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] TMOD4
    2333 ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] TMOD3
    2334 tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] TMOD1
    2335 sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] SNX9
    2336 neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] TMOD2
    2337 homeobox protein dlx-2. [swissprot;acc:q07687] DLX2
    2338 homeobox protein dlx-5. [swissprot;acc:p56178] DLX5
    2339 fetal brain protein 239 (239fb). [swissprot;acc:q15777] MPPED2
    2340 homeobox protein dlx-3. [swissprot;acc:o60479] DLX3
    2341 activated p21cdc42hs kinase. [refseq;acc:nm_005781] TNK2
    2342 mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093] MAP3K7IP2
    2343 glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] no value 212.222 1.00451 211.27
    2344 kccr13l. [refseq;acc:nm_139179] DAGLB 219.878 1.0045 218.893
    2345 dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609] RAD51
    2346 serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] NEK1 217.057 1.00448 218.03
    2347 serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [swissprot;acc:p51956] NEK3
    2348 glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406] GAPDH
    2349 fibulin-1 precursor. [swissprot;acc:p23142] FBLN1 192.348 1.00441 191.503
    2350 cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4] CNDP2 209.811 1.00439 210.733

    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/