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 Hugo Network Comparison Type description Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1851 to 1900 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		description
    		Value Type
    		Interaction Map
    		red
    		network_comparison
    		green
    116 PANK1 Divided pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Measured High confidence 21185 1.34491 28492
    PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Rooted Low confidence 66.9562 1.08017 72.3243
    RGL1 Subtracted ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Measured High confidence 13261.9 2244.1 11017.8
    SLC16A7 monocarboxylate transporter 2 (mct 2). [swissprot;acc:o60669] Squared Low confidence 62451.1 8222 70673.1
    SLC7A13 amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817] Measured 6991.78 856.67 7848.45
    VPS18 Divided vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Ranked 204.161 1.07008 190.791
    117 ABRA Subtracted striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] 225.495 13.966 211.529
    CPSF3 Divided cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Squared High confidence 211446 1.53866 137422
    F13A1 coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] Ranked Low confidence 226.395 1.06935 211.713
    GATAD2B Subtracted transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Squared High confidence 81888.8 25582.3 56306.5
    GNB4 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Rooted 40.5691 15.1428 25.4263
    HMG20A Divided high-mobility group 20a. [refseq;acc:nm_018200] Low confidence 69.2016 1.08014 74.7475
    Subtracted Ranked High confidence 208.588 36.81 171.778
    JUNB Divided transcription factor jun-b. [swissprot;acc:p17275] Rooted 63.4173 1.25409 79.5311
    MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Measured Low confidence 11285.3 1.0937 10318.5
    NEURL neuralized-like. [refseq;acc:nm_004210] Ranked High confidence 332.326 1.24491 266.948
    PANK2 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Measured 21185 1.34491 28492
    PITRM1 Subtracted metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 9276.47 2186.1 7090.37
    SLC11A1 natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] Rooted Low confidence 63.7749 5.6766 69.4515
    SLC16A8 monocarboxylate transporter 3 (mct 3). [swissprot;acc:o95907] Squared 62413.6 8203.8 70617.4
    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] Measured 6991.78 856.67 7848.45
    TMED10 Divided transmembrane protein tmp21 precursor (21 kda transmembrane trafficking protein) (p24delta) (s31iii125) (s31i125) (tmp-21-i). [swissprot;acc:p49755] Squared 81950.4 1.14622 93933.1
    118 no value Subtracted tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] High confidence 81888.8 25582.3 56306.5
    ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Measured 9275.1 2185.45 7089.65
    HOMER2 Divided homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Rooted 50.3065 1.2519 62.9788
    NDN necdin. [swissprot;acc:q99608] Measured Low confidence 11285.3 1.0937 10318.5
    NDUFA12 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] Ranked High confidence 284.753 1.24382 228.934
    Subtracted Rooted 37.2205 14.9859 52.2064
    OSR1 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Ranked 274.027 36.237 237.79
    PANK3 Divided pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Measured 21185 1.34491 28492
    PAPOLA poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Squared 210445 1.53858 136779
    PIGB phosphatidylinositol glycan, class b. [refseq;acc:nm_004855] Low confidence 81950.4 1.14622 93933.1
    SENP8 sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] Rooted 67.0736 1.08012 72.4478
    SLC11A2 Subtracted natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] 64.1217 5.5783 69.7
    SLC16A3 monocarboxylate transporter 4 (mct 4) (mct 3). [swissprot;acc:o15427] Squared 62293.5 8145.5 70439
    SLC7A11 cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] Measured 6991.78 856.67 7848.45
    SPOCK1 testican-1 precursor (spock protein). [swissprot;acc:q08629] Ranked 220.254 13.857 234.111
    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] 226.395 1.06935 211.713
    119 ACADVL Subtracted acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Measured High confidence 12998.5 2139.7 15138.2
    ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] Ranked 281.582 35.211 246.371
    ATP5H atp synthase d chain, mitochondrial (ec 3.6.3.14) (my032 protein). [swissprot;acc:o75947] Squared Low confidence 59868.5 8108.9 51759.6
    CDK3 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] High confidence 81606.8 25391 56215.8
    COQ7 Divided ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Rooted 50.3247 1.25166 62.9892
    EXOC2 exocyst complex component sec5. [swissprot;acc:q96kp1] Squared 210335 1.53848 136716
    MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Measured Low confidence 11285.3 1.0937 10318.5
    NDUFS4 nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Ranked High confidence 318.982 1.23157 259.004
    NEDD8 ubiquitin-like protein nedd8. [swissprot;acc:q15843] Rooted Low confidence 67.0736 1.08012 72.4478
    OPHN1 Subtracted oligophrenin 1. [swissprot;acc:o60890] 61.0103 5.5701 66.5804
    PCF11 Divided pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Squared 58331.7 1.14295 51036
    PPP2R1B Subtracted serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] Rooted High confidence 63.6507 14.938 48.7127

    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/