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 Rank Gene Hugo Value Type Network Comparison Type Interaction Map red Filtered network_comparison green
    Results: HTML CSV LaTeX Showing element 1980 to 2029 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		network_comparison
    		green
    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 1.01097 216.074
    peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] 1010 CROT 217.523 1.03264 210.648
    peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] 841 PEX19 198.781 1.04259 190.66
    peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] 2177 PXMP2 210.961 1.00667 209.563
    peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] 1147 PEX14 208.651 1.02729 203.109
    peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] 1362 PAOX 228.644 1.02194 223.736
    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 1.0577 216.576
    peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [swissprot;acc:o00628] 2447 PEX7 206.084 1.00324 206.752
    peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] 351 PEX1 242.14 1.09728 265.696
    pescadillo homolog 1. [swissprot;acc:o00541] 515 PES1 251.297 1.06962 234.941
    phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] 1082 PLEKHF2 220.118 1.03011 213.685
    phd finger protein 9. [refseq;acc:nm_018062] 1345 FANCL 216.772 1.02224 221.594
    phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] 235 PAH 227.357 1.11785 254.15
    phenylalanine-trna synthetase. [refseq;acc:nm_006567] 895 FARS2 217.491 1.03902 209.323
    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 1.00459 213.235
    phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] 2220 PNMT 221.509 1.00637 220.108
    phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] 403 PDC 207.908 1.08807 226.218
    phosducin-like protein (phlp). [swissprot;acc:q13371] 400 PDCL
    phosphate carrier protein, mitochondrial precursor (ptp). [swissprot;acc:q00325] 3176 SLC25A3 0.00001 1 0.00001
    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 1.00309 205.286
    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 1.00319 205.371
    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 1 0.00001
    phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] 1651 PIK3R1 219.062 1.01445 215.942
    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 1 0.00001
    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 1.00787 214.28
    phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing gamma polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-gamma) (ptdins-3-kinase c2 gamma) (pi3k-c2gamma). [swissprot;acc:o75747] 2079 PIK3C2G
    phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492] 1391 PICALM 218.47 1.02148 213.875
    phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 627 JMJD6 214.256 1.05994 202.139
    phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] 1774 PGM3 223.032 1.01214 225.739
    phosphofurin acidic cluster sorting protein 1 isoform 1; cytosolic sorting protein pacs-1. [refseq;acc:nm_018026] 2805 PACS1 0.00001 1 0.00001
    phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] 2362 PGK1 207.178 1.00415 208.037
    phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] 2359 PGK2 207.196 208.056
    phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] 1233 no value 212.724 1.0245 207.637
    phosphoglycerate mutase 2 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme m) (pgam-m) (bpg-dependent pgam 2) (muscle-specific phosphoglycerate mutase). [swissprot;acc:p15259] 1234 PGAM2
    phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [refseq;acc:nm_002645] 2082 PIK3C2A 215.967 1.00787 214.28
    phosphoinositide-3-kinase, class 3; vps34; phosphatidylinositol 3-kinase, class 3. [refseq;acc:nm_002647] 3173 PIK3C3 0.00001 1 0.00001
    phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [swissprot;acc:q13393] 2287 PLD1 206.475 1.00535 205.376
    phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939] 2296 PLD2 206.451 1.00521 205.38
    phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7] 1915 PLSCR2 215.747 1.01019 213.571
    phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] 1913 no value 215.745 1.01021 213.564
    phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2] 1914 PLSCR4
    phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] 758 PLTP 224.434 1.04968 235.583
    phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] 1602 PMM1 217.334 1.01599 213.914
    phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] 1601 PMM2 217.268 1.01602 213.842
    phosphoribosyl pyrophosphate synthetase-associated protein 1 (prpp synthetase-associated protein 1) (39 kda phosphoribosypyrophosphate synthetase-associated protein) (pap39). [swissprot;acc:q14558] 2869 PRPSAP1 0.00001 1 0.00001
    phosphoribosyl pyrophosphate synthetase-associated protein 2 (prpp synthetase-associated protein 2) (41 kda phosphoribosypyrophosphate synthetase-associated protein) (pap41). [swissprot;acc:o60256] 2943 PRPSAP2
    phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] 739 PFAS 223.58 1.0512 235.027

    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/