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 [...,...].
    Gene Rank description Hugo Network Comparison Type red Value Type Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 2051 to 2100 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		Value Type
    		Interaction Map
    		green
    		network_comparison
    257 cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286] no value 68.3669 Rooted Low confidence 72.2396 1.05665
    dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] DDOST 200.691 Ranked High confidence 179.88 1.11569
    glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] GYS2 53244.4 Squared Low confidence 48813.4 1.09077
    huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] no value 15482.3 High confidence 20162.4 1.30229
    synaptojanin 1 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 1). [swissprot;acc:o43426] SYNJ1 8082.34 Measured Low confidence 8579.93 1.06157
    tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] TPM3 201.316 Ranked 192.404 1.04632
    258 adp-ribosylation factor guanine nucleotide factor 6; hepatocellular carcinoma-associated antigen 67. [refseq;acc:nm_015310] PSD3 50448.8 Squared 46264.1 1.09045
    aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] AKR7A3 9249.74 Measured 9818.95 1.06154
    homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] CUTL2 6417.33 High confidence 7857.93 1.22449
    huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] HIP1 76438 Squared 58889.7 1.29799
    max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] MXD4 227.999 Ranked 204.366 1.11564
    thrombospondin 3 precursor. [swissprot;acc:p49746] THBS3 51.6132 Rooted 45.8422 1.12589
    tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] TPM1 201.304 Ranked Low confidence 192.427 1.04613
    ubiquitin-conjugating enzyme e2 g1 (ec 6.3.2.19) (ubiquitin-protein ligase g1) (ubiquitin carrier protein g1) (e217k) (ubc7). [swissprot;acc:q99462] UBE2G1 70.3765 Rooted 74.3627 1.05664
    259 goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] COL4A3BP 76360.8 Squared High confidence 58841.7 1.29773
    max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] RAB24 227.999 Ranked 204.37 1.11562
    neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] WASL 6417.81 Measured 7852.52 1.22355
    oligophrenin 1. [swissprot;acc:o60890] OPHN1 6428.7 Low confidence 6824.22 1.06152
    parafibromin. [refseq;acc:nm_024529] CDC73 67.6012 Rooted 71.4286 1.05662
    trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] PDSS1 211.794 Ranked 202.482 1.04599
    trs85 homolog. [swissprot;acc:q9y2l5] KIAA1012 50448.8 Squared 46264.1 1.09045
    tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] TFIP11 58.2964 Rooted High confidence 65.5926 1.12516
    260 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] AKR7A2 9246.23 Measured Low confidence 9814.59 1.06147
    ankyrin repeat domain protein 7 (testis-specific protein tsa806). [swissprot;acc:q92527] ANKRD7 216.855 Ranked 207.34 1.04589
    c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] HS3ST6 219.421 High confidence 196.978 1.11394
    calcineurin b subunit isoform 1 (protein phosphatase 2b regulatory subunit 1) (protein phosphatase 3 regulatory subunit b alpha isoform 1). [swissprot;acc:p06705] WDR92 67.4201 Rooted Low confidence 71.2324 1.05655
    huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] HIP1R 76296.4 Squared High confidence 58801.6 1.29752
    leukemia-associated protein with a cxxc domain. [sptrembl;acc:q8nfu7] CXXC6 50448.8 Low confidence 46264.1 1.09045
    multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] SCYE1 59.0951 Rooted High confidence 66.4332 1.12417
    signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] SRP9 4244.95 Measured 5193.42 1.22343
    261 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] FDX1 8837.18 Low confidence 9379.17 1.06133
    ba526d8.2 (novel protein similar to kiaa1074). [sptrembl;acc:q9h560] ANKRD19 216.845 Ranked 207.333 1.04588
    heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] HS3ST3A1 219.421 High confidence 196.978 1.11394
    pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] PC 48127.9 Squared 62245.6 1.29334
    ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] RRM2B 62.3337 Rooted 70.0738 1.12417
    sec7 homolog; adp-ribosylation factor guanine nucleotide-exchange factor 6. [refseq;acc:nm_012455] PSD4 50448.8 Squared Low confidence 46264.1 1.09045
    signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] SRP9 4247.36 Measured High confidence 5192.61 1.22255
    trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] PDSS1 67.7274 Rooted Low confidence 71.5408 1.05631
    262 ariadne-1 protein homolog (ari-1) (ubiquitin-conjugating enzyme e2- binding protein 1) (ubch7-binding protein) (ubcm4-interacting protein) (hhari) (h7-ap2) (hussy-27) (mop-6). [swissprot;acc:q9y4x5] ARIH1 56512.1 Squared 51843.6 1.09005
    breast cancer antigen ny-br-1. [refseq;acc:nm_052997] ANKRD30A 216.842 Ranked 207.332 1.04587
    cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] CPSF4 24896.4 Measured High confidence 20431.7 1.21852
    heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] HS3ST3B1 219.421 Ranked 196.978 1.11394
    neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] CHRNA7 26157.6 Squared 20236.2 1.29261
    oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] ARHGAP26 6440.08 Measured Low confidence 6834.37 1.06122
    polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] POLI 59.4073 Rooted High confidence 66.7002 1.12276
    udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] GALE 70.6152 Low confidence 74.5839 1.0562
    263 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] ADCY6 26157.6 Squared High confidence 20236.2 1.29261
    coiled-coil protein bicd2; homolog of drosophila bicaudal d. [refseq;acc:nm_015250] BICD2 70.75 Rooted Low confidence 74.7143 1.05603
    heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] HS3ST2 219.421 Ranked High confidence 196.978 1.11394
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] STT3A 7424.14 Measured Low confidence 7877.49 1.06106

    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/