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 [...,...].
    Value Type Gene Filtered Rank Network Comparison Type red Interaction Map green network_comparison description
    Results: HTML CSV LaTeX Showing element 501 to 550 of 19268 in total
    Value Type  : Ranked
    Filtered  : 0
    Rank
    Network Comparison Type
    red
    Interaction Map
    green
    network_comparison
    description
    126 Divided 9722.71 High confidence 11493.8 1.18216 ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858]
    14899.4 Low confidence 17562.2 1.17872 bromodomain adjacent to zinc finger domain protein 1a (atp-utilizing chromatin assembly and remodeling factor 1) (hacf1) (atp-dependent chromatin remodelling protein) (williams syndrome transcription factor-related chromatin remodeling factor 180) (wcrf180) (hwalp1) (chrac subunit acf1) (hspc317). [swissprot;acc:q9nrl2]
    Subtracted 12314.9 High confidence 10489.3 1825.6 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]
    15945.5 Low confidence 14123.3 1822.2 putative protein-tyrosine phosphatase tpte (ec 3.1.3.48). [swissprot;acc:p56180]
    127 Divided 9411.34 High confidence 11119.7 1.18152 trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]
    10041.1 Low confidence 11814.4 1.1766 scribble. [refseq;acc:nm_015356]
    Subtracted 11732 High confidence 13530.6 1798.6 ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]
    16660.8 Low confidence 18475.5 1814.7 dna helicase homolog (fragment). [sptrembl;acc:q9y645]
    128 Divided 9259.51 10879.6 1.17496 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]
    11564.4 High confidence 9794.29 1.18073 60s ribosomal protein l39. [swissprot;acc:p02404]
    Subtracted 9722.71 11493.8 1771.09 ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858]
    11161.3 Low confidence 12965.5 1804.2 lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]
    129 Divided 9248.93 10865.5 1.17478 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]
    14222.5 High confidence 12058.6 1.17945 isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]
    Subtracted 11564.4 9794.29 1770.11 60s ribosomal protein l39. [swissprot;acc:p02404]
    13206.7 Low confidence 15008.1 1801.4 piwi-like 2; miwi like. [refseq;acc:nm_018068]
    130 Divided 14476.2 High confidence 17069.5 1.17914 enigma protein; lim domain protein. [refseq;acc:nm_005451]
    16024.9 Low confidence 13646 1.17433 sedlin. [swissprot;acc:o14582]
    Subtracted 10041.1 11814.4 1773.3 scribble. [refseq;acc:nm_015356]
    14922.7 High confidence 13174.5 1748.2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]
    131 Divided 4793.5 Low confidence 5609 1.17013 mitochondrial 39s ribosomal protein l39 (l39mt) (mrp-l39) (mrp-l5) (pred22 protein). [swissprot;acc:q9nyk5]
    8375.43 High confidence 9873.58 1.17887 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]
    Subtracted 14951.6 13204.2 1747.4 integral membrane protein cii-3b. [sptrembl;acc:o75609]
    15039.8 Low confidence 13277.6 1762.2 transcription factor bteb4 (basic transcription element binding- protein 4) (bte-binding protein 4) (krueppel-like factor 16) (novel sp1-like zinc finger transcription factor 2) (transcription factor nslp2). [swissprot;acc:q9bxk1]
    132 Divided 16411.9 14027.1 1.17001 mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]
    19048 High confidence 22389 1.1754 rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]
    Subtracted 10883 12622.8 1739.8 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]
    12716.5 Low confidence 10962.4 1754.1 glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]
    133 Divided 6814 High confidence 8009 1.17537 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]
    11236.1 Low confidence 13113.5 1.16709 alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745]
    Subtracted 14922.7 13174.5 1748.2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]
    17144.8 High confidence 15405.6 1739.2 mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362]
    134 Divided 9210.38 Low confidence 7893.05 1.1669 sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]
    12314.9 High confidence 10489.3 1.17404 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]
    Subtracted 12157.6 13890.3 1732.7 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]
    16853 Low confidence 15123 1730 maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]
    135 Divided 12314.9 High confidence 10489.3 1.17404 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]
    15432.9 Low confidence 13250 1.16475 phosphatidylinositol 4-kinase alpha (ec 2.7.1.67) (pi4-kinase) (ptdins-4-kinase) (pi4k-alpha). [swissprot;acc:p42356]
    Subtracted 8871.11 High confidence 10603.2 1732.09 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132]
    16853 Low confidence 15123 1730 serpin b11. [swissprot;acc:q96p15]
    136 Divided 12024.2 13977.2 1.16242 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]
    12335.3 High confidence 10506.8 1.17403 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2]
    Subtracted 12759.4 11028.8 1730.6 polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]
    16853 Low confidence 15123 1730 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]
    137 Divided 11161.3 12965.5 1.16165 lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]
    12328.5 High confidence 10501 1.17403 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6]
    Subtracted 16853 15123 1730 maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]
    19314 Low confidence 21041 1727 homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
    138 Divided 8730 7516 1.16152 zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]
    12384.7 High confidence 10549.4 1.17397 likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033]

    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/