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 [...,...].
    Gene description Rank Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 451 to 500 of 3228 in total
    Value Type  : Measured
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		red
    		green
    		network_comparison
    bup protein. [refseq;acc:nm_012071] 2911 0.00001 0.00001 1
    bystin. [swissprot;acc:q13895] 950 4280.99 4697.02 1.09718
    c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586] 2102 4860.34 5127.3 1.05493
    c-jun-amino-terminal kinase interacting protein 3 (jnk-interacting protein 3) (jip-3) (jnk map kinase scaffold protein 3) (mitogen- activated protein kinase 8-interacting protein 3). [swissprot;acc:q9upt6] 1962 5941.24 6297.78 1.06001
    c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 1638 9895.77 9248.18 1.07002
    c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 1630 9903.22 9253.79 1.07018
    c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 488 10872.4 12447 1.14483
    c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] 1528 5869.97 6301.24 1.07347
    c18b11 homolog (44.9kd). [refseq;acc:nm_152260] 707 5317.78 5944.25 1.11781
    c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] 2120 6951.29 7329 1.05434
    c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 2174 3641.45 3463.02 1.05152
    c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 2421 7355.46 7088.93 1.0376
    ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 874 9921.43 10941.2 1.10278
    caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844] 941 4970.21 5455.34 1.09761
    cab2. [refseq;acc:nm_033419] 2618 5599.85 5683 1.01485
    cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708] 1217 6021.21 6536.45 1.08557
    cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] 1723 5458.12 5830.76 1.06827
    calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] 1356 5657.71 6103.57 1.07881
    calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [swissprot;acc:q14206] 1360 5657.72 6103.52 1.07879
    calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8] 1361
    calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746] 1913 6858.84 7287.27 1.06246
    calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [swissprot;acc:q9ujs0] 1916
    calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] 440 6251.91 7192.08 1.15038
    calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] 606 6148.94 6955.76 1.13121
    calcium/calmodulin-dependent protein kinase type ii alpha chain (ec 2.7.1.123) (cam-kinase ii alpha chain) (cam kinase ii alpha subunit) (camk-ii alpha subunit). [swissprot;acc:q9uqm7] 1385 6079.45 6555.4 1.07829
    calcium/calmodulin-dependent protein kinase type ii beta chain (ec 2.7.1.123) (cam-kinase ii beta chain) (cam kinase ii beta subunit) (camk-ii beta subunit). [swissprot;acc:q13554] 1386 6079.46 6555.41
    calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [swissprot;acc:q13557] 1376
    calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [swissprot;acc:q13555] 1375 6079.45 6555.4
    calcyphosine. [swissprot;acc:q13938] 365 5189 6088.47 1.17334
    calmegin precursor. [swissprot;acc:o14967] 1473 5910.06 6355.08 1.0753
    calmodulin. [swissprot;acc:p02593] 2928 0.00001 0.00001 1
    calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] 1474 5910.06 6355.08 1.0753
    calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 2384 4164.96 4336.92 1.04129
    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] 2383 4164.76 4337.01 1.04136
    calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797] 1526 5369.1 5763.72 1.0735
    calsyntenin-1 precursor. [swissprot;acc:o94985] 536 10603.5 12069.5 1.13826
    calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 541 10600.3 12065.2 1.13819
    calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 543 10599.9 12064.7
    camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] 1439 5658.8 6093.56 1.07683
    camp responsive element binding protein-like 2. [refseq;acc:nm_001310] 3078 0.00001 0.00001 1
    camp-dependent protein kinase type i-alpha regulatory chain (tissue- specific extinguisher-1) (tse1). [swissprot;acc:p10644] 3089
    camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] 1710 5916.13 6321.77 1.06857
    camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] 1715 5918.48 6323.83 1.06849
    camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612] 1714 5917.23 6322.73 1.06853
    camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694] 1713
    camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 1712
    candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] 2025 4813.13 5091.36 1.05781
    carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] 2351 8353.97 8001.45 1.04406
    carboxypeptidase a5. [refseq;acc:nm_080385] 2344
    carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] 2345

    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/