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 51 to 100 of 8289 in total
    Value Type  : Measured
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    26 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] High confidence 1833.01 892.67 2.0534
    sperm associated antigen 7. [refseq;acc:nm_004890] Low confidence 23318 19280.8 1.20939
    27 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] High confidence 1834.33 895.134 2.04922
    protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Low confidence 3840.85 4614.87 1.20152
    28 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] High confidence 1834.36 895.194 2.04912
    tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Low confidence 3098.94 3719.66 1.2003
    29 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] High confidence 1834.52 895.507 2.04858
    tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Low confidence 3121.28 3739.84 1.19818
    30 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] 36474.3 43509.4 1.19288
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] High confidence 1834.59 895.633 2.04837
    31 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 1834.63 895.697 2.04827
    vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Low confidence 36469.3 43503.3 1.19287
    32 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] High confidence 1834.73 895.893 2.04793
    nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence 36360.3 43368.8 1.19275
    33 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] High confidence 1835.3 896.972 2.04611
    vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Low confidence 36360.3 43368.8 1.19275
    34 guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] High confidence 1836.71 907.546 2.02382
    protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Low confidence 5339.5 6352.4 1.1897
    35 deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 33111.4 39358.1 1.18866
    guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] High confidence 1836.71 907.564 2.02378
    36 guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] 1836.76 907.741 2.02344
    proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Low confidence 6462.09 7593.77 1.17513
    37 guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] High confidence 1836.76 907.763 2.02339
    jun dimerization protein. [refseq;acc:nm_130469] Low confidence 6462.09 7593.77 1.17513
    38 guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] High confidence 1836.76 907.774 2.02337
    rab11-family interacting protein 4. [refseq;acc:nm_032932] Low confidence 7407.56 8696.7 1.17403
    39 eferin. [swissprot;acc:o75154]
    guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] High confidence 1836.8 907.903 2.02312
    40 fos-related antigen 2. [swissprot;acc:p15408] Low confidence 6480.59 7600.25 1.17277
    guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] High confidence 1836.81 907.978 2.02297
    41 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]
    protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Low confidence 6481.62 7600.61 1.17264
    42 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 6485.05 7601.81 1.17221
    guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] High confidence 1857.32 958.237 1.93827
    43 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Low confidence 13689.1 11788.6 1.16122
    guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] High confidence 1881.02 1027.36 1.83093
    44 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] 1931.34 1057.39 1.82652
    transcription factor jun-d. [swissprot;acc:p17535] Low confidence 6614.51 7680.25 1.16112
    45 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] High confidence 1926.69 1056.02 1.82448
    transcription factor jun-b. [swissprot;acc:p17275] Low confidence 6613.42 7678.76 1.16109
    46 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] High confidence 779.167 1390.33 1.78438
    transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867] Low confidence 8313.02 9645.34 1.16027
    47 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] High confidence 779.167 1390.33 1.78438
    nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236] Low confidence 8313.02 9645.34 1.16027
    48 doc-1 related protein (doc-1r). [swissprot;acc:o75956] High confidence 779.167 1390.33 1.78438
    transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] Low confidence 8313.02 9645.34 1.16027
    49 microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 13470.1 11654.4 1.1558
    neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] High confidence 779.167 1390.33 1.78438
    50 microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Low confidence 13466.8 11652.4 1.15571
    neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] High confidence 779.167 1390.33 1.78438

    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/