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 2330 to 2379 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    2330 phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] FARSB 214.213 213.235 1.00459
    2331 mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] MIZF 229.258 230.294 1.00452
    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 212.222 211.27 1.00451
    2344 kccr13l. [refseq;acc:nm_139179] DAGLB 219.878 218.893 1.0045
    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 217.057 218.03 1.00448
    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 192.348 191.503 1.00441
    2350 cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4] CNDP2 209.811 210.733 1.00439
    2351 synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] SYT12 214.223 213.289 1.00438
    2352 copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [swissprot;acc:q04656] ATP7A 215.088 214.155 1.00436
    2353 electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117] ETFB 182.232 183.027
    2354 copper-transporting atpase 2 (ec 3.6.3.4) (copper pump 2) (wilson disease-associated protein). [swissprot;acc:p35670] ATP7B 215.078 214.148 1.00434
    2355 26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665] PSMD7 217.232 218.162 1.00428
    2356 importin 4. [refseq;acc:nm_024658] no value 220.921 221.863 1.00426
    2357 ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [swissprot;acc:p56554] UBE2G2 198.181 197.346 1.00423
    2358 38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318] FKBP8
    2359 phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] PGK2 207.196 208.056 1.00415
    2360 gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] ENO2 207.186 208.046
    2361 beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] ENO3
    2362 phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] PGK1 207.178 208.037
    2363 alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] ENO1 207.186 208.046
    2364 transaldolase (ec 2.2.1.2). [swissprot;acc:p37837] TALDO1 212.816 213.697 1.00414
    2365 glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] CNDP1 208.958 209.82 1.00413
    2366 14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] HRSP12 203.353 202.529 1.00407
    2367 26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231] PSMD11 217.589 218.475
    2368 26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460] PSMD1 218.555 219.434 1.00402
    2369 adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186] ADRM1
    2370 ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5] UCHL5
    2371 rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763] C19orf2
    2372 mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796] SMAD2 212.724 213.574 1.004
    2373 mothers against decapentaplegic homolog 1 (smad 1) (mothers against dpp homolog 1) (mad-related protein 1) (transforming growth factor- beta signaling protein-1) (bsp-1) (hsmad1) (jv4-1). [swissprot;acc:q15797] SMAD1
    2374 cop9 subunit 6 (mov34 homolog, 34 kd). [refseq;acc:nm_006833] COPS6
    2375 mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [swissprot;acc:q92940] SMAD3
    2376 histone deacetylase 11 (hd11). [swissprot;acc:q96db2] HDAC11
    2377 ethanolamine kinase-like protein eki2 (flj10761). [swissprot;acc:q9nvf9] ETNK2
    2378 ethanolamine kinase (ec 2.7.1.82) (eki). [swissprot;acc:q9hbu6] ETNK1
    2379 hepatocellular carcinoma susceptibility protein; x 003 protein; hdcmc29p; hspc260; likely ortholog of mouse cd40 ligand-activated specific transcript 3 (clast3). [refseq;acc:nm_020232] TNFSF5IP1

    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/