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 2382 to 2431 of 3228 in total
    Value Type  : Measured
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		red
    		green
    		network_comparison
    2382 hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3] 4457.6 4642.72 1.04153
    2383 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] 4164.76 4337.01 1.04136
    2384 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 4164.96 4336.92 1.04129
    2385 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] 3716.43 3569.68 1.04111
    2386 60s ribosomal protein l30. [swissprot;acc:p04645] 3674.02 3529.35 1.04099
    2387 cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] 8265.85 7940.87 1.04092
    2388 diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] 4418.21 4594.87 1.03998
    2389 lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234] 6327.14 6579.38 1.03987
    2390 tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258]
    2391 defender against cell death 1 (dad-1). [swissprot;acc:p46966]
    2392 t-complex 11. [refseq;acc:nm_018679]
    2393 tubulin gamma-2 chain (gamma-2 tubulin). [swissprot;acc:q9nrh3]
    2394 trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102] 5502.5 5721.43 1.03979
    2395 homeobox protein otx2. [swissprot;acc:p32243] 5682 5905.08 1.03926
    2396 myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572] 6711.27 6974.49 1.03922
    2397 yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906] 6707.29 6970.07 1.03918
    2398 hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775]
    2399 homeobox protein otx1. [swissprot;acc:p32242] 5691.1 5913.92 1.03915
    2400 malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] 4368.44 4539.34 1.03912
    2401 cone-rod homeobox protein. [swissprot;acc:o43186] 5694.04 5916.78
    2402 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] 5078.5 5275.76 1.03884
    2403 40s ribosomal protein s21. [swissprot;acc:p35265]
    2404 cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453]
    2405 maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]
    2406 bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595]
    2407 plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120]
    2408 serpin b11. [swissprot;acc:q96p15]
    2409 placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237]
    2410 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]
    2411 leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740]
    2412 dynactin 4. [refseq;acc:nm_032486] 4644.04 4470.47 1.03883
    2413 cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059] 6956.32 7223.14 1.03836
    2414 alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443]
    2415 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] 6956.62 7223.09 1.0383
    2416 dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] 8048.38 7752.09 1.03822
    2417 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 3598.55 3467.65 1.03775
    2418 60s acidic ribosomal protein p1. [swissprot;acc:p05386] 4857.03 5039.78 1.03763
    2419 thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243]
    2420 thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599]
    2421 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 7355.46 7088.93 1.0376
    2422 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]
    2423 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]
    2424 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]
    2425 mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]
    2426 tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] 6123.47 6351.84 1.03729
    2427 mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] 5333.6 5531.41 1.03709
    2428 fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] 7243.19 7509.81 1.03681
    2429 fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114]
    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

    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/