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 [...,...].
    description Gene Rank Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1958 to 2007 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] 1555 PASK 196.192 192.996 1.01656
    paxillin. [swissprot;acc:p49023] 436 PXN 221.522 205.286 1.07909
    pbk1 protein. [sptrembl;acc:o76021] 983 RSL1D1 243.312 235.353 1.03382
    pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] 833 PSIP1 231.734 222.222 1.0428
    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] 914 GOPC 210.863 218.878 1.03801
    pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] 925 PEF1 215.665 207.942 1.03714
    pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] 2460 no value 235.812 235.088 1.00308
    peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] 928 MTRF1 225.976 218.017 1.03651
    peptide deformylase, mitochondrial precursor (ec 3.5.1.88) (pdf) (polypeptide deformylase). [swissprot;acc:q9hbh1] 2884 PDF 0.00001 0.00001 1
    peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] 1753 MSRA 220.091 217.362 1.01256
    peptidyl prolyl isomerase h; cyclophilin h. [refseq;acc:nm_006347] 1939 PPIH 198.258 196.319 1.00988
    peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] 2400 PPIB 182.4 183.083 1.00374
    peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] 1078 PPIE 174.387 179.697 1.03045
    peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526] 2076 PIN1 221.703 223.483 1.00803
    peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] 695 PPIL4 226.135 214.405 1.05471
    peregrin (bromodomain and phd finger-containing protein 1) (br140 protein). [swissprot;acc:p55201] 2820 no value 0.00001 0.00001 1
    pericentrin 1; frount; nucleoporin nup75. [refseq;acc:nm_024844] 3015 NUP85
    peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] 673 CASK 226.497 214.355 1.05664
    peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162] 2573 PRDX4 213.347 213.005 1.00161
    peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [swissprot;acc:p30044] 1124 PRDX5 207.553 213.256 1.02748
    peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] 2688 no value 194.557 194.392 1.00085
    peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] 1851 ACOT4 218.448 216.08 1.01096
    peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] 1849 ACOT1 218.445 216.074 1.01097
    peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] 1010 CROT 217.523 210.648 1.03264
    peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] 841 PEX19 198.781 190.66 1.04259
    peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] 2177 PXMP2 210.961 209.563 1.00667
    peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] 1147 PEX14 208.651 203.109 1.02729
    peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] 1362 PAOX 228.644 223.736 1.02194
    peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] 664 PEX5 229.072 216.576 1.0577
    peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [swissprot;acc:o00628] 2447 PEX7 206.084 206.752 1.00324
    peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] 351 PEX1 242.14 265.696 1.09728
    pescadillo homolog 1. [swissprot;acc:o00541] 515 PES1 251.297 234.941 1.06962
    phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] 1082 PLEKHF2 220.118 213.685 1.03011
    phd finger protein 9. [refseq;acc:nm_018062] 1345 FANCL 216.772 221.594 1.02224
    phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] 235 PAH 227.357 254.15 1.11785
    phenylalanine-trna synthetase. [refseq;acc:nm_006567] 895 FARS2 217.491 209.323 1.03902
    phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] 894 FARSA
    phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] 2330 FARSB 214.213 213.235 1.00459
    phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] 2220 PNMT 221.509 220.108 1.00637
    phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] 403 PDC 207.908 226.218 1.08807
    phosducin-like protein (phlp). [swissprot;acc:q13371] 400 PDCL
    phosphate carrier protein, mitochondrial precursor (ptp). [swissprot;acc:q00325] 3176 SLC25A3 0.00001 0.00001 1
    phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [swissprot;acc:q92903] 2459 CDS1 204.653 205.286 1.00309
    phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674] 2449 CDS2 204.717 205.371 1.00319
    phosphatidylethanolamine-binding protein (pebp) (prostatic binding protein) (hcnppp) (neuropolypeptide h3) (raf kinase inhibitor protein) (rkip) [contains: hippocampal cholinergic neurostimulating peptide (hcnp)]. [swissprot;acc:p30086] 3162 PEBP1 0.00001 0.00001 1
    phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] 1651 PIK3R1 219.062 215.942 1.01445
    phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459] 1656 PIK3R2
    phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569] 1653 PIK3R3
    phosphatidylinositol glycan class t precursor. [refseq;acc:nm_015937] 3024 PIGT 0.00001 0.00001 1
    phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] 2080 PIK3C2B 215.967 214.28 1.00787

    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
    - Hugo is the HGNC identifier if it exists
    - 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/