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 2008 to 2057 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		network_comparison
    		green
    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 215.967 1.00787 214.28
    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
    phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] 1754 PSAT1 220.091 1.01256 217.362
    pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059] 1250 LIMS1 219.354 1.02437 224.7
    pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] 993 PNN 211.071 1.03362 204.205
    placenta growth factor precursor (plgf). [swissprot;acc:p49763] 3036 PGF 0.00001 1 0.00001
    placental protein 11 precursor (ec 3.4.21.-) (pp11). [swissprot;acc:p21128] 3076 no value
    placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] 796 SERPINB6 224.244 1.04578 234.511
    plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] 510 CPB2 177.699 1.07057 190.24
    plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] 794 SERPINB8 224.244 1.04578 234.511
    platelet-activating factor acetylhydrolase ib alpha subunit (ec 3.1.1.47) (paf acetylhydrolase 45 kda subunit) (paf-ah 45 kda subunit) (paf-ah alpha) (pafah alpha) (lissencephaly-1 protein) (lis- 1). [swissprot;acc:p43034] 3221 PAFAH1B1 0.00001 1 0.00001
    pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832] 1259 PLEKHC1 219.354 1.02437 224.7
    pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 522 PLRG1 222.893 1.06891 208.523
    pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] 2094 PMS2 207.321 1.00765 205.747
    pnas-18. [sptrembl;acc:q9bzu3] 1463 no value 161.056 1.01959 164.211
    pogo transposable element with znf domain isoform 1. [refseq;acc:nm_015100] 2932 POGZ 0.00001 1 0.00001
    poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] 1464 no value 217.351 1.01957 213.18
    poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] 984 PAPOLA 116.71 1.03379 120.654
    poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] 994 PAPOLG 116.845 1.03361 120.772
    polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940] 1700 PABPC1 217.624 1.01367 214.69
    polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] 1696 PABPC3
    polyadenylate-binding protein 4 (poly(a)-binding protein 4) (pabp 4) (inducible poly(a)-binding protein) (ipabp) (activated-platelet protein-1) (app-1). [swissprot;acc:q13310] 1699 PABPC4
    polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] 1368 SMOX 228.644 1.02194 223.736
    polybromo 1. [refseq;acc:nm_018165] 2591 PBRM1 220.02 1.00147 219.696
    polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710] 784 PQBP1 224.385 1.04789 235.131
    polyhomeotic like 3; early development regulator 3; polyhomeotic 3. [refseq;acc:nm_024947] 2809 PHC3 0.00001 1 0.00001
    polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 435 POLI 221.522 1.07909 205.286
    polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] 2095 POLS 229.266 1.00763 227.53
    polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] 429 POLR3G 239.709 1.08064 259.038
    polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] 451 POLR3C 239.092 1.07785 257.705

    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/