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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2430 to 2479 of 3228 in total
    Value Type  : Measured
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		red
    		green
    		network_comparison
    2430 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 7243.07 7509.58 1.0368
    2431 fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] 7242.75 7508.98 1.03676
    2432 gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] 8154.48 8453.84 1.03671
    2433 mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] 4585.86 4753.26 1.0365
    2434 wd repeat domain 26. [refseq;acc:nm_025160] 6423.46 6655.9 1.03619
    2435 activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482] 3669.33 3797.78 1.03501
    2436 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 3708.67 3584.47 1.03465
    2437 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]
    2438 rna, u transporter 1; snurportin-1. [refseq;acc:nm_005701] 7139.06 7384.85 1.03443
    2439 putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] 3754.39 3629.51 1.03441
    2440 u3 snornp protein 4 homolog. [refseq;acc:nm_033416] 4730.66 4891.26 1.03395
    2441 adapter-related protein complex 3 mu 2 subunit (clathrin coat assembly protein ap47 homolog 2) (clathrin coat associated protein ap47 homolog 2) (golgi adaptor ap-1 47 kda protein homolog 2) (ha1 47 kda subunit homolog 2) (clathrin assembly protein assembly protein complex 1 medium chain homolog 2) (p47b). [swissprot;acc:p53677] 6477.82 6695.58 1.03362
    2442 breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] 5454.62 5637.88 1.0336
    2443 skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643] 3634.59 3756.67 1.03359
    2444 adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2] 6478.14 6695.67 1.03358
    2445 skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192] 3633.14 3754.96 1.03353
    2446 dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] 4031.94 4166.99 1.0335
    2447 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] 3730.53 3611.05 1.03309
    2448 40s ribosomal protein s16. [swissprot;acc:p17008]
    2449 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] 3730.74 3611.45 1.03303
    2450 pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] 6737.15 6957.34 1.03268
    2451 2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [swissprot;acc:p12694]
    2452 succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] 6042.36 6237.19 1.03224
    2453 conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7] 6931.15 7152.73 1.03197
    2454 homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] 8751.01 8480.03 1.03196
    2455 prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] 5978.83 6166.89 1.03145
    2456 pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399]
    2457 yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] 4998.72 5155.87 1.03144
    2458 presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] 4751.74 4900.37 1.03128
    2459 gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080]
    2460 presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]
    2461 phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] 5114.15 5272.92 1.03105
    2462 bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939]
    2463 multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234]
    2464 dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.12) (e2) (pdc-e2) (70 kda mitochondrial autoantigen of primary biliary cirrhosis) (pbc) (m2 antigen complex 70 kda subunit). [swissprot;acc:p10515] 6291.2 6486.07 1.03098
    2465 germ cell-less. [refseq;acc:nm_022471] 7764.92 8003.67 1.03075
    2466 pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [swissprot;acc:p40424] 7765.3 8004 1.03074
    2467 pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426]
    2468 hyporthetical protein mgc27169. [refseq;acc:nm_176782]
    2469 homeobox protein meis1. [swissprot;acc:o00470]
    2470 homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770]
    2471 bag-family molecular chaperone regulator-2. [swissprot;acc:o95816]
    2472 pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425]
    2473 pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245]
    2474 homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687]
    2475 zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] 3573.66 3682.14 1.03036
    2476 zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] 3569.07 3676.7 1.03016
    2477 zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] 3568.84 3676.43 1.03015
    2478 zinc finger protein 232. [swissprot;acc:q9uny5] 3568.96 3676.57
    2479 zinc finger protein 99. [refseq;acc:nm_032164] 3568.99 3676.6

    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
    - 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/