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 2232 to 2281 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    2232 RAPSN 43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] 215.547 214.194 1.00632
    2233 TRIM3 tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [swissprot;acc:o75382] 202.414 203.691 1.00631
    2234 no value seven in absentia homolog 1. [refseq;acc:nm_003031] 223.608 225.005 1.00625
    2235 RARS2 arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] 200.95 199.711 1.0062
    2236 no value protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] 222.959 224.337 1.00618
    2237 BRD3 bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] 222.965 224.343
    2238 BRD4 bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885] 222.959 224.337
    2239 BRDT testis-specific bromodomain protein. [refseq;acc:nm_001726] 222.958 224.336
    2240 LRRC4 nag14 protein. [refseq;acc:nm_022143] 222.959 224.337
    2241 BRD2 bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] 222.96 224.338
    2242 ITM2B integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] 209.197 207.915 1.00617
    2243 ITM2C integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7]
    2244 ITM2A integral membrane protein 2a (e25 protein). [swissprot;acc:o43736]
    2245 FBLN2 fibulin-2 precursor. [swissprot;acc:p98095] 191.618 190.448 1.00614
    2246 MRPL18 mitochondrial ribosomal protein l18. [refseq;acc:nm_014161] 223.58 224.943 1.0061
    2247 ADI1 sipl protein. [refseq;acc:nm_018269] 208.609 207.346 1.00609
    2248 KIF3C kinesin-like protein kif3c. [swissprot;acc:o14782] 219.045 220.377 1.00608
    2249 PC pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] 181.091 179.999 1.00607
    2250 CSTF2T likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] 164.064 165.058 1.00606
    2251 ENOPH1 e-1 enzyme. [refseq;acc:nm_021204] 208.315 207.061
    2252 ALAD delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] 217.185 218.498 1.00605
    2253 KIF3B kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [swissprot;acc:o15066] 219.047 220.371 1.00604
    2254 no value ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] 193.065 194.22 1.00598
    2255 ZFHX3 alpha-fetoprotein enhancer binding protein (at motif-binding factor) (at-binding transcription factor 1). [swissprot;acc:q15911] 202.366 203.57 1.00595
    2256 SIAH2 seven in absentia homolog 2. [refseq;acc:nm_005067] 223.546 224.869 1.00592
    2257 QPRT nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] 212.563 211.315 1.00591
    2258 CDC37 hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 223.888 225.191 1.00582
    2259 DMC1 meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565] 213.391 214.606 1.00569
    2260 TSEN34 leng5 protein. [refseq;acc:nm_024075] 221.599 220.351 1.00566
    2261 WARS tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381]
    2262 no value ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]
    2263 WARS2 tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6]
    2264 no value thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]
    2265 MAD2L1 mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257] 211.597 210.416 1.00561
    2266 ATP13A2 probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11]
    2267 TBP tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226]
    2268 TRIM2 tripartite motif protein 2. [swissprot;acc:q9c040] 202.312 203.437 1.00556
    2269 PSMD10 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] 217.419 218.627
    2270 MMS19 mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] 207.54 208.69 1.00554
    2271 FMO5 dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] 216.622 215.436 1.00551
    2272 FMO6P putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774]
    2273 MAP3K7IP1 mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750] 213.015 211.858 1.00546
    2274 PGD 6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [swissprot;acc:p52209] 213.642 214.801 1.00542
    2275 DHDDS dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887] 207.319 208.44 1.00541
    2276 FMO3 dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] 216.613 215.448
    2277 RCC1 regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] 191.936 190.909 1.00538
    2278 ZEB2 zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [swissprot;acc:o60315]
    2279 ZEB1 transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275]
    2280 PSMA7 proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818] 212.793 211.657 1.00537
    2281 SRRM2 splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [refseq;acc:nm_016333] 219.652 218.482 1.00536

    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/