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 description Value Type Interaction Map Gene Network Comparison Type red green Filtered network_comparison
    Results: HTML CSV LaTeX Showing element 101 to 150 of 19268 in total
    Value Type  : Ranked
    Rank
    		description
    		Interaction Map
    		Network Comparison Type
    		red
    		green
    		Filtered
    		network_comparison
    13 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence Divided 37.9984 29.1831 1 1.30207
    protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] High confidence 288.754 212.554 1.3585
    Low confidence Subtracted 255.046 202.362 52.684
    sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796] Divided 7435.56 12191.6 0 1.63963
    14 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] Subtracted 286.396 238.476 1 47.92
    ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 13730.5 8257 0 5473.5
    cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] High confidence Divided 56.6768 75.3531 1 1.32952
    dystrophin. [swissprot;acc:p11532] 10232.5 18054.8 0 1.76446
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Subtracted 266.863 336.191 1 69.328
    ptd016 protein. [refseq;acc:nm_016125] Low confidence Divided 18050 11234 0 1.60673
    ubiquitin protein ligase. [refseq;acc:nm_130466] High confidence Subtracted 7523 15339.2 7816.2
    vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Low confidence Divided 37.9984 29.1831 1 1.30207
    15 adenomatous polyposis coli like. [refseq;acc:nm_005883] 12074.1 7597.61 0 1.5892
    camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211] Subtracted 13109 18516 5407
    cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] 286.347 238.454 1 47.893
    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] High confidence 22422 14964 0 7458
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 266.863 336.19 1 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
    protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Low confidence 255.046 202.362 1.26035
    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] High confidence 19403 11267 0 1.72211
    16 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Low confidence 7395 11625 1.57201
    cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] High confidence 12170.7 20670.6 1.69839
    cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973] Low confidence Subtracted 284.798 237.743 1 47.055
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] High confidence 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 18050 11234 0 6816
    sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796] Low confidence 7435.56 12191.6 4756.04
    thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Divided 305.472 247.246 1 1.2355
    17 bcl2-related ovarian killer. [refseq;acc:nm_032515] Subtracted 265.638 223.235 42.403
    cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] High confidence Divided 56.7841 75.447 1.32866
    ero1-like. [refseq;acc:nm_014584] Subtracted 13853 20536 0 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
    Low confidence Subtracted 4731
    gbp protein isoform a. [refseq;acc:nm_017870] Divided 305.399 247.213 1 1.23537
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] High confidence Subtracted 266.864 336.182 69.318
    leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] Low confidence Divided 8082.33 5266.67 0 1.53462
    18 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] High confidence 185.678 245.247 1 1.32082
    early hematopoietic zinc finger. [refseq;acc:nm_015461] Low confidence 5850.23 8903.28 0 1.52187
    elongation of very long chain fatty acids protein 2. [swissprot;acc:q9nxb9] Subtracted 16116.4 11505 4611.4
    fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] High confidence 7509.39 14178.1 6668.71
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 266.865 336.181 1 69.316
    homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Divided 22286 13216 0 1.68629
    jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Low confidence 305.303 247.169 1 1.2352
    protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Subtracted 273.188 232.49 40.698
    19 alpha 2 globin. [refseq;acc:nm_000517] 11486.2 15987.1 0 4500.9
    glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] High confidence Divided 185.678 245.247 1 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
    histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773] Low confidence 188.298 228.509 40.211
    homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] High confidence Divided 22286 13216 0 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

    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/