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 Filtered Interaction Map red green network_comparison
    Results: HTML CSV LaTeX Showing element 1575 to 1624 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    description
    Interaction Map
    red
    green
    network_comparison
    788 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Low confidence 200.788 195.605 1.0265
    hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] High confidence 138.705 132.538 1.04653
    789 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] 224.244 234.511 1.04578
    polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481] Low confidence 205.859 200.547 1.02649
    790 40s ribosomal protein s21. [swissprot;acc:p35265] High confidence 224.244 234.511 1.04578
    eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Low confidence 200.79 195.608 1.02649
    791 cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] High confidence 224.244 234.511 1.04578
    similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428] Low confidence 205.859 200.547 1.02649
    792 hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] 204.204 198.939 1.02647
    maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] High confidence 224.244 234.511 1.04578
    793 bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595]
    similar to atp/gtp-binding protein. [sptrembl;acc:q8nem8] Low confidence 184.195 179.447 1.02646
    794 plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] High confidence 224.244 234.511 1.04578
    trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Low confidence 184.195 179.447 1.02646
    795 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] 202.525 197.308 1.02644
    serpin b11. [swissprot;acc:q96p15] High confidence 224.244 234.511 1.04578
    796 grancalcin. [swissprot;acc:p28676] Low confidence 202.524 197.308 1.02644
    placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] High confidence 224.244 234.511 1.04578
    797 asc-1 complex subunit p100. [refseq;acc:nm_032204] Low confidence 211.636 206.184 1.02644
    cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] High confidence 224.244 234.511 1.04578
    798 leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740]
    sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Low confidence 202.524 197.308 1.02644
    799 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 201.294 196.11 1.02643
    sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] High confidence 221.965 212.404 1.04501
    800 nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307]
    rp42 homolog; squamous cell carcinoma-related oncogene. [refseq;acc:nm_020640] Low confidence 202.755 197.536 1.02642
    801 beta-catenin (pro2286). [swissprot;acc:p35222] High confidence 224.445 214.894 1.04445
    programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Low confidence 202.522 197.311 1.02641
    802 dc12 protein. [refseq;acc:nm_020187] 203.345 198.117 1.02639
    testis-specific protein tex28. [swissprot;acc:o15482] High confidence 212.386 221.785 1.04425
    803 dolichyl-diphosphooligosaccharide--protein glycosyltransferase 67 kda subunit precursor (ec 2.4.1.119) (ribophorin i) (rpn-i). [swissprot;acc:p04843] Low confidence 199.573 194.441 1.02639
    similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] High confidence 212.386 221.785 1.04425
    804 a kindred of iglon. [refseq;acc:nm_173808]
    elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Low confidence 204.519 199.267 1.02636
    805 ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] High confidence 212.386 221.785 1.04425
    synaptojanin 1 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 1). [swissprot;acc:o43426] Low confidence 198.496 193.399 1.02635
    806 inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] High confidence 212.386 221.785 1.04425
    vacuolar atp synthase subunit c (ec 3.6.3.14) (v-atpase c subunit) (vacuolar proton pump c subunit). [swissprot;acc:p21283] Low confidence 202.369 197.173 1.02635
    807 myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572] 200.782 195.631 1.02633
    palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] High confidence 212.386 221.785 1.04425
    808 beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115]
    vigilin (high density lipoprotein-binding protein) (hdl-binding protein). [swissprot;acc:q00341] Low confidence 201.169 196.014 1.0263
    809 serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] 202.744 197.552 1.02628
    syntaxin 16 (syn16). [swissprot;acc:o14662] High confidence 212.386 221.785 1.04425
    810 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]
    amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905] Low confidence 196.326 191.3 1.02627
    811 syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] High confidence 212.386 221.785 1.04425
    syntaxin 1b. [swissprot;acc:q15531] Low confidence 211.432 206.021 1.02626
    812 alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920] High confidence 212.386 221.785 1.04425
    zinc transporter 1 (znt-1). [swissprot;acc:q9y6m5] Low confidence 206.173 200.909 1.0262

    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/