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 Network Comparison Type Hugo Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2230 to 2279 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    2230 ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890] UFD1L 217.955 219.336 1.00634
    2231 hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431] SYVN1 221.842 223.246 1.00633
    2232 43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] RAPSN 215.547 214.194 1.00632
    2233 tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [swissprot;acc:o75382] TRIM3 202.414 203.691 1.00631
    2234 seven in absentia homolog 1. [refseq;acc:nm_003031] no value 223.608 225.005 1.00625
    2235 arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] RARS2 200.95 199.711 1.0062
    2236 protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] no value 222.959 224.337 1.00618
    2237 bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] BRD3 222.965 224.343
    2238 bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885] BRD4 222.959 224.337
    2239 testis-specific bromodomain protein. [refseq;acc:nm_001726] BRDT 222.958 224.336
    2240 nag14 protein. [refseq;acc:nm_022143] LRRC4 222.959 224.337
    2241 bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] BRD2 222.96 224.338
    2242 integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] ITM2B 209.197 207.915 1.00617
    2243 integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] ITM2C
    2244 integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] ITM2A
    2245 fibulin-2 precursor. [swissprot;acc:p98095] FBLN2 191.618 190.448 1.00614
    2246 mitochondrial ribosomal protein l18. [refseq;acc:nm_014161] MRPL18 223.58 224.943 1.0061
    2247 sipl protein. [refseq;acc:nm_018269] ADI1 208.609 207.346 1.00609
    2248 kinesin-like protein kif3c. [swissprot;acc:o14782] KIF3C 219.045 220.377 1.00608
    2249 pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] PC 181.091 179.999 1.00607
    2250 likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] CSTF2T 164.064 165.058 1.00606
    2251 e-1 enzyme. [refseq;acc:nm_021204] ENOPH1 208.315 207.061
    2252 delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] ALAD 217.185 218.498 1.00605
    2253 kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [swissprot;acc:o15066] KIF3B 219.047 220.371 1.00604
    2254 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] no value 193.065 194.22 1.00598
    2255 alpha-fetoprotein enhancer binding protein (at motif-binding factor) (at-binding transcription factor 1). [swissprot;acc:q15911] ZFHX3 202.366 203.57 1.00595
    2256 seven in absentia homolog 2. [refseq;acc:nm_005067] SIAH2 223.546 224.869 1.00592
    2257 nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] QPRT 212.563 211.315 1.00591
    2258 hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] CDC37 223.888 225.191 1.00582
    2259 meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565] DMC1 213.391 214.606 1.00569
    2260 leng5 protein. [refseq;acc:nm_024075] TSEN34 221.599 220.351 1.00566
    2261 tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381] WARS
    2262 ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] no value
    2263 tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6] WARS2
    2264 thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] no value
    2265 mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257] MAD2L1 211.597 210.416 1.00561
    2266 probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11] ATP13A2
    2267 tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226] TBP
    2268 tripartite motif protein 2. [swissprot;acc:q9c040] TRIM2 202.312 203.437 1.00556
    2269 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] PSMD10 217.419 218.627
    2270 mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] MMS19 207.54 208.69 1.00554
    2271 dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] FMO5 216.622 215.436 1.00551
    2272 putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774] FMO6P
    2273 mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750] MAP3K7IP1 213.015 211.858 1.00546
    2274 6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [swissprot;acc:p52209] PGD 213.642 214.801 1.00542
    2275 dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887] DHDDS 207.319 208.44 1.00541
    2276 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] FMO3 216.613 215.448
    2277 regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] RCC1 191.936 190.909 1.00538
    2278 zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [swissprot;acc:o60315] ZEB2
    2279 transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275] ZEB1

    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/