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 Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 101 to 150 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    51 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] JPH2 Low confidence 234.802 260.98 1.11149
    spermatogenesis associated 6. [refseq;acc:nm_019073] SPATA6 High confidence 133 105 1.26667
    52 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] AMPD2
    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] SMPD2 Low confidence 234.802 260.98 1.11149
    53 db83 protein. [swissprot;acc:p57088] TMEM33
    transcription factor jun-b. [swissprot;acc:p17275] JUNB High confidence 201.144 158.868 1.26611
    54 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] CPEB3 Low confidence 267.448 240.822 1.11056
    transcription factor jun-d. [swissprot;acc:p17535] JUND High confidence 200.941 158.941 1.26425
    55 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] CPEB4 Low confidence 267.376 240.78 1.11046
    protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] PRKRAP1 High confidence 320.927 254.434 1.26134
    56 brachyury protein (t protein). [swissprot;acc:o15178] T Low confidence 224.922 202.592 1.11022
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] no value High confidence 266.856 336.233 1.25998
    57 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] GNG12
    proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] FOS Low confidence 202.802 182.73 1.10985
    58 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] GNG4 High confidence 266.863 336.191 1.25979
    jun dimerization protein. [refseq;acc:nm_130469] no value Low confidence 202.802 182.73 1.10985
    59 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] GNG3 High confidence 266.863 336.19 1.25978
    nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] NDUFA12 Low confidence 233.134 210.267 1.10875
    60 fos-related antigen 2. [swissprot;acc:p15408] FOSL2 202.793 182.961 1.10839
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] GNG8 High confidence 266.864 336.184 1.25976
    61 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] GNG5 336.182 1.25975
    protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] FOSB Low confidence 202.792 182.974 1.10831
    62 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] FOSL1 202.79 183.017 1.10804
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] GNG10 High confidence 266.865 336.181 1.25974
    63 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] no value 336.178 1.25973
    putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] RBM7 Low confidence 265.688 239.902 1.10749
    64 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] GNG11 High confidence 266.868 336.159 1.25965
    transcription factor jun-d. [swissprot;acc:p17535] JUND Low confidence 202.709 183.361 1.10552
    65 guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] GNAQ High confidence 267.136 336.077 1.25807
    transcription factor jun-b. [swissprot;acc:p17275] JUNB Low confidence 202.728 183.388 1.10546
    66 guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] GNA11 High confidence 267.136 336.077 1.25807
    mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] MTUS1 Low confidence 221.902 200.783 1.10518
    67 guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] GNAT2 High confidence 267.14 336.075 1.25805
    retinoblastoma-associated factor 600. [refseq;acc:nm_020765] UBR4 Low confidence 165.535 149.799 1.10505
    68 60s ribosomal protein l37a. [swissprot;acc:p12751] no value 239.692 217.005 1.10455
    guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] GNAZ High confidence 267.139 336.075 1.25805
    69 guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] GNAT1 267.14
    testis-specific protein tex28. [swissprot;acc:o15482] TEX28P2 Low confidence 259.517 235.017 1.10425
    70 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] GOSR2
    guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] GNAI2 High confidence 267.142 336.074 1.25804
    71 cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] no value Low confidence 230.944 209.149 1.10421
    guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] GNAI1 High confidence 267.144 336.073 1.25802
    72 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] GNAI3
    set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] SMYD2 Low confidence 230.944 209.149 1.10421
    73 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] JPH3 High confidence 288 362 1.25694
    set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] SMYD1 Low confidence 230.944 209.149 1.10421
    74 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] JPH2 High confidence 288 362 1.25694
    putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] AHCYL1 Low confidence 195.817 215.516 1.1006
    75 nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] GBAS 249.709 226.944 1.10031
    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] SMPD2 High confidence 288 362 1.25694

    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/