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 [...,...].
    Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 30 to 79 of 7460 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Rank
    description
    Network Comparison Type
    Filtered
    red
    green
    network_comparison
    8 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted 0 22286 13216 9070
    junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 288 362 74
    nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Divided 0 11525 21888 1.89918
    9 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Subtracted 22286 13216 9070
    junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1 288 362 74
    transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Divided 0 11525 21888 1.89918
    xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 1 212 309 1.45755
    10 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 0 7509.39 14178.1 1.88805
    protein x 0004. [refseq;acc:nm_016301] 1 212 309 1.45755
    pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Subtracted 0 20989 12479 8510
    sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] 1 288 362 74
    11 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 0 12170.7 20670.6 8499.9
    db83 protein. [swissprot;acc:p57088] 1 288 362 74
    potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Divided 0 11627 6248 1.86092
    rad50-interacting protein 1. [refseq;acc:nm_021930] 1 337 232 1.45259
    12 folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 0 9429.18 5208.84 1.81023
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Subtracted 1 266.856 336.233 69.377
    rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Divided 337 232 1.45259
    succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Subtracted 0 19403 11267 8136
    13 dystrophin. [swissprot;acc:p11532] 10232.5 18054.8 7822.3
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] 1 266.856 336.233 69.377
    heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Divided 0 5210.5 9264.5 1.77804
    protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 1 288.754 212.554 1.3585
    14 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 56.6768 75.3531 1.32952
    dystrophin. [swissprot;acc:p11532] 0 10232.5 18054.8 1.76446
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Subtracted 1 266.863 336.191 69.328
    ubiquitin protein ligase. [refseq;acc:nm_130466] 0 7523 15339.2 7816.2
    15 guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] 22422 14964 7458
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 1 266.863 336.19 69.327
    microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Divided 56.7244 75.3948 1.32914
    succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] 0 19403 11267 1.72211
    16 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 12170.7 20670.6 1.69839
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Subtracted 1 266.864 336.184 69.32
    microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Divided 56.7252 75.3954 1.32913
    ptd016 protein. [refseq;acc:nm_016125] Subtracted 0 18050 11234 6816
    17 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Divided 1 56.7841 75.447 1.32866
    ero1-like. [refseq;acc:nm_014584] Subtracted 0 13853 20536 6683
    fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Divided 11543 6812 1.69451
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Subtracted 1 266.864 336.182 69.318
    18 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Divided 185.678 245.247 1.32082
    fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Subtracted 0 7509.39 14178.1 6668.71
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 1 266.865 336.181 69.316
    homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Divided 0 22286 13216 1.68629
    19 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 1 185.678 245.247 1.32082
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Subtracted 266.865 336.178 69.313
    homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided 0 22286 13216 1.68629
    nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Subtracted 4475.84 11083.9 6608.06
    20 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Divided 1 185.678 245.247 1.32082
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Subtracted 266.868 336.159 69.291
    homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Divided 0 22286 13216 1.68629

    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/