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 2258 to 2307 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    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
    2280 proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818] PSMA7 212.793 211.657 1.00537
    2281 splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [refseq;acc:nm_016333] SRRM2 219.652 218.482 1.00536
    2282 splicing factor u2af 35 kda subunit (u2 auxiliary factor 35 kda subunit) (u2 snrnp auxiliary factor small subunit). [swissprot;acc:q01081] U2AF1
    2283 proteasome subunit alpha type 7-like (ec 3.4.25.1). [swissprot;acc:q8taa3] PSMA8 212.81 211.676
    2284 rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] no value 219.652 218.482
    2285 splicing factor u2af 65 kda subunit (u2 auxiliary factor 65 kda subunit) (u2 snrnp auxiliary factor large subunit) (hu2af(65)). [swissprot;acc:p26368] U2AF2
    2286 dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] FMO2 216.608 215.456 1.00535
    2287 phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [swissprot;acc:q13393] PLD1 206.475 205.376
    2288 dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] FMO1 216.607 215.458 1.00533
    2289 dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] FMO4 216.605 215.46 1.00531
    2290 myo-inositol 1-phosphate synthase a1. [refseq;acc:nm_016368] no value 200.158 201.213 1.00527
    2291 arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681]
    2292 ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441] UBL4A
    2293 large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [swissprot;acc:p46379] no value
    2294 protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] PPP1R13B 162.331 163.187
    2295 tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] TP53BP2 162.86 163.712 1.00523
    2296 phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939] PLD2 206.451 205.38 1.00521
    2297 epsin 3. [refseq;acc:nm_017957] EPN3 218.153 219.284 1.00518
    2298 ubiquitin-like protein smt3c precursor (ubiquitin-homology domain protein pic1) (ubiquitin-like protein ubl1) (ubiquitin-related protein sumo-1) (gap modifying protein 1) (gmp1) (sentrin). [swissprot;acc:q93068] SUMO1P3 215.239 216.339 1.00511
    2299 udp-glucose 6-dehydrogenase (ec 1.1.1.22) (udp-glc dehydrogenase) (udp-glcdh) (udpgdh). [swissprot;acc:o60701] UGDH
    2300 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] ACAA1 191.563 192.541
    2301 nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] NMNAT3 217.392 218.498 1.00509
    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 191.571 192.544 1.00508
    2307 camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] PRKAR2A 215.554 214.467 1.00507

    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/