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 1462 to 1511 of 3228 in total
    Value Type  : Measured
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		red
    		green
    		network_comparison
    1462 transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472] 5672.24 6103.99 1.07612
    1463 collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955] 5672.2 6103.92 1.07611
    1464 zasp protein (fragment). [sptrembl;acc:q9y4z3] 5671.93 6103.49 1.07609
    1465 glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695] 5686.74 6119.36 1.07608
    1466 proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [swissprot;acc:p28074] 6523.17 7019.44
    1467 p47 protein isoform a. [refseq;acc:nm_016143] 6444.4 6932.39 1.07572
    1468 sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901] 5473.09 5887.45 1.07571
    1469 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]
    1470 ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181]
    1471 40s ribosomal protein s8. [swissprot;acc:p09058] 5659.45 6087.55 1.07564
    1472 26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008] 5984.47 6435.42 1.07535
    1473 calmegin precursor. [swissprot;acc:o14967] 5910.06 6355.08 1.0753
    1474 calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824]
    1475 soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]
    1476 rna (guanine-7-) methyltransferase. [refseq;acc:nm_003799]
    1477 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] 3687.37 3429.37 1.07523
    1478 cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] 5659.22 6084.68 1.07518
    1479 hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] 5787.03 6221.72 1.07511
    1480 cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] 5660.17 6085.22 1.07509
    1481 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] 3688.8 3431.33 1.07504
    1482 leng5 protein. [refseq;acc:nm_024075] 5372.25 5775.21 1.07501
    1483 tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381]
    1484 ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]
    1485 tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6]
    1486 thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]
    1487 nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] 5573.64 5991.58 1.07499
    1488 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]
    1489 vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [swissprot;acc:p46459] 6192.38 6656.34 1.07492
    1490 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] 6340.5 6815.41 1.0749
    1491 fidgetin-like 1. [refseq;acc:nm_022116] 6057.46 6510.9 1.07486
    1492 dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] 4619.81 4965.45 1.07482
    1493 deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366] 6146.36 6606.21
    1494 kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145] 4619.81 4965.45
    1495 nadh-ubiquinone oxidoreductase pdsw subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-pdsw) (ci-pdsw). [swissprot;acc:o96000] 6362.92 6838.6 1.07476
    1496 apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797] 5945.56 6389.63 1.07469
    1497 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 6339.08 6812.45 1.07467
    1498 40s ribosomal protein s13. [swissprot;acc:q02546] 5414.98 5818.7 1.07456
    1499 hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] 5798.31 6230.55 1.07455
    1500 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] 10075.5 9377.75 1.0744
    1501 coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678]
    1502 coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3]
    1503 coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444]
    1504 peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9]
    1505 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299]
    1506 hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6] 6152.78 6610.46 1.07439
    1507 atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766]
    1508 guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3]
    1509 acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763] 7237.39 7775.21 1.07431
    1510 60s ribosomal protein l21. [swissprot;acc:p46778] 5546.11 5957.99 1.07426
    1511 serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] 7234.61 7771.58 1.07422

    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/