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 Value Type Hugo Network Comparison Type description Interaction Map Filtered network_comparison red green
    Results: HTML CSV LaTeX Showing element 1841 to 1890 of 66312 in total
    Filtered  : 1
    Rank
    		Value Type
    		Hugo
    		Network Comparison Type
    		description
    		Interaction Map
    		network_comparison
    		red
    		green
    116 Measured no value Divided hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Low confidence 1.0937 11285.3 10318.5
    PANK1 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] High confidence 1.34491 21185 28492
    RGL1 Subtracted ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] 2244.1 13261.9 11017.8
    SLC7A13 amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817] Low confidence 856.67 6991.78 7848.45
    Ranked no value testican-3 precursor. [swissprot;acc:q9bq16] 13.994 220.395 234.389
    GNB3 Divided guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] High confidence 1.24545 268.565 334.483
    HMG20B Subtracted high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] 36.925 208.52 171.595
    VPS18 Divided vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Low confidence 1.07008 204.161 190.791
    Squared FKBP8 38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318] 1.14667 52687.3 45948.1
    GATAD2A Subtracted p66 alpha. [refseq;acc:nm_017660] High confidence 25582.3 81888.8 56306.5
    MYH13 Divided myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 1.54043 19321 12542.6
    SLC16A7 Subtracted monocarboxylate transporter 2 (mct 2). [swissprot;acc:o60669] Low confidence 8222 62451.1 70673.1
    Rooted AMPD2 Divided amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] High confidence 1.26165 80.4705 101.526
    GNB1 Subtracted guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] 15.185 40.6302 25.4452
    HMG20B high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Low confidence 5.6978 69.0515 74.7493
    PSEN1 Divided presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 1.08017 66.9562 72.3243
    117 Measured MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 1.0937 11285.3 10318.5
    PANK2 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] High confidence 1.34491 21185 28492
    PITRM1 Subtracted metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 2186.1 9276.47 7090.37
    SLC7A7 y+l amino acid transporter 1 (y(+)l-type amino acid transporter 1) (y+lat-1) (y+lat1) (monocyte amino acid permease 2) (mop-2). [swissprot;acc:q9um01] Low confidence 856.67 6991.78 7848.45
    Ranked ABRA striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] 13.966 225.495 211.529
    F13A1 Divided coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] 1.06935 226.395 211.713
    HMG20A Subtracted high-mobility group 20a. [refseq;acc:nm_018200] High confidence 36.81 208.588 171.778
    NEURL Divided neuralized-like. [refseq;acc:nm_004210] 1.24491 332.326 266.948
    Squared CPSF3 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] 1.53866 211446 137422
    GATAD2B Subtracted transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] 25582.3 81888.8 56306.5
    SLC16A8 monocarboxylate transporter 3 (mct 3). [swissprot;acc:o95907] Low confidence 8203.8 62413.6 70617.4
    TMED10 Divided transmembrane protein tmp21 precursor (21 kda transmembrane trafficking protein) (p24delta) (s31iii125) (s31i125) (tmp-21-i). [swissprot;acc:p49755] 1.14622 81950.4 93933.1
    Rooted GNB4 Subtracted guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] High confidence 15.1428 40.5691 25.4263
    HMG20A Divided high-mobility group 20a. [refseq;acc:nm_018200] Low confidence 1.08014 69.2016 74.7475
    JUNB transcription factor jun-b. [swissprot;acc:p17275] High confidence 1.25409 63.4173 79.5311
    SLC11A1 Subtracted natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] Low confidence 5.6766 63.7749 69.4515
    118 Measured ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] High confidence 2185.45 9275.1 7089.65
    NDN Divided necdin. [swissprot;acc:q99608] Low confidence 1.0937 11285.3 10318.5
    PANK3 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] High confidence 1.34491 21185 28492
    SLC7A11 Subtracted cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] Low confidence 856.67 6991.78 7848.45
    Ranked NDUFA12 Divided 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] High confidence 1.24382 284.753 228.934
    OSR1 Subtracted odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 36.237 274.027 237.79
    SPOCK1 testican-1 precursor (spock protein). [swissprot;acc:q08629] Low confidence 13.857 220.254 234.111
    TGM1 Divided protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] 1.06935 226.395 211.713
    Squared no value Subtracted tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] High confidence 25582.3 81888.8 56306.5
    PAPOLA Divided poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] 1.53858 210445 136779
    PIGB phosphatidylinositol glycan, class b. [refseq;acc:nm_004855] Low confidence 1.14622 81950.4 93933.1
    SLC16A3 Subtracted monocarboxylate transporter 4 (mct 4) (mct 3). [swissprot;acc:o15427] 8145.5 62293.5 70439
    Rooted HOMER2 Divided homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] High confidence 1.2519 50.3065 62.9788
    NDUFA12 Subtracted 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] 14.9859 37.2205 52.2064
    SENP8 Divided sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] Low confidence 1.08012 67.0736 72.4478
    SLC11A2 Subtracted natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] 5.5783 64.1217 69.7
    119 Measured ACADVL acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] High confidence 2139.7 12998.5 15138.2
    MAGED1 Divided melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Low confidence 1.0937 11285.3 10318.5

    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/