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 2025 to 2074 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] 1602 PMM1 217.334 213.914 1.01599
    phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] 1601 PMM2 217.268 213.842 1.01602
    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 0.00001 1
    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 223.58 235.027 1.0512
    phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] 1754 PSAT1 220.091 217.362 1.01256
    pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059] 1250 LIMS1 219.354 224.7 1.02437
    pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] 993 PNN 211.071 204.205 1.03362
    placenta growth factor precursor (plgf). [swissprot;acc:p49763] 3036 PGF 0.00001 0.00001 1
    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 224.244 234.511 1.04578
    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 177.699 190.24 1.07057
    plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] 794 SERPINB8 224.244 234.511 1.04578
    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 0.00001 1
    pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832] 1259 PLEKHC1 219.354 224.7 1.02437
    pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 522 PLRG1 222.893 208.523 1.06891
    pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] 2094 PMS2 207.321 205.747 1.00765
    pnas-18. [sptrembl;acc:q9bzu3] 1463 no value 161.056 164.211 1.01959
    pogo transposable element with znf domain isoform 1. [refseq;acc:nm_015100] 2932 POGZ 0.00001 0.00001 1
    poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] 1464 no value 217.351 213.18 1.01957
    poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] 984 PAPOLA 116.71 120.654 1.03379
    poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] 994 PAPOLG 116.845 120.772 1.03361
    polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940] 1700 PABPC1 217.624 214.69 1.01367
    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 228.644 223.736 1.02194
    polybromo 1. [refseq;acc:nm_018165] 2591 PBRM1 220.02 219.696 1.00147
    polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710] 784 PQBP1 224.385 235.131 1.04789
    polyhomeotic like 3; early development regulator 3; polyhomeotic 3. [refseq;acc:nm_024947] 2809 PHC3 0.00001 0.00001 1
    polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 435 POLI 221.522 205.286 1.07909
    polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] 2095 POLS 229.266 227.53 1.00763
    polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] 429 POLR3G 239.709 259.038 1.08064
    polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] 451 POLR3C 239.092 257.705 1.07785
    polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863] 1204 KCTD13 219.022 213.607 1.02535
    polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780] 953 EXOSC10 198.494 205.466 1.03512
    polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481] 1811 GALNT2 216.854 214.35 1.01168
    polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765] 1412 REEP5 206.102 210.42 1.02095
    polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] 1414 REEP6
    polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190] 1382 PTBP2 218.47 213.876 1.02148
    polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599] 1394 PTBP1 213.875
    ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] 918 SORBS1 212.952 205.292 1.03731
    porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397] 2708 HMBS 227.796 227.66 1.0006
    possible global transcription activator snf2l1. [swissprot;acc:p28370] 2594 SMARCA1 220.02 219.696 1.00147
    possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531] 2596 SMARCA2
    possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532] 2593 SMARCA4
    postsynaptic protein cript; hspc139 protein. [refseq;acc:nm_014171] 3034 CRIPT 0.00001 0.00001 1
    potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [refseq;acc:nm_020122] 2119 KCMF1 221.248 222.788 1.00696
    potassium channel tetramerisation domain containing 3; ny-ren-45 antigen. [refseq;acc:nm_016121] 2975 KCTD3 0.00001 0.00001 1
    potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 145 KCNIP4 265.639 319.546 1.20293
    potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] 475 KCNA1 226.727 210.816 1.07547

    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/