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 Network Comparison Type Hugo Value Type description Interaction Map Filtered network_comparison red green
    Results: HTML CSV LaTeX Showing element 1525 to 1574 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		Interaction Map
    		network_comparison
    		red
    		green
    191 ICK Squared intestinal cell kinase isoform a; mak-related kinase; serine/threonine protein kinase. [refseq;acc:nm_014920] Low confidence 1.10897 45402.8 50350.5
    PLDN Rooted pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] High confidence 1.14995 63.1192 72.584
    SF3B1 Measured splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 1.27712 4638.1 5923.4
    SLC15A2 Ranked oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Low confidence 1.05224 201.43 191.43
    192 AQP2 Squared aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] High confidence 1.34524 71387.4 96033.4
    ARAF Measured a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 1.26767 17757.5 14008
    MSI2 Ranked musashi 2 isoform a. [refseq;acc:nm_138962] 1.14055 227.491 199.458
    NOX5 Rooted nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] Low confidence 1.06154 69.9161 74.2187
    RC3H2 Ranked membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] 1.05214 217.341 206.571
    SF4 Rooted splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] High confidence 1.14877 53.6107 61.5862
    SHOC2 Squared leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Low confidence 1.10896 51506.6 46445.8
    TRMU Measured trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] 1.07469 9385.4 10086.4
    193 HBS1L Ranked hbs1-like. [refseq;acc:nm_006620] 1.05213 206.166 216.913
    HRAS Squared transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] 1.10862 51484.4 46440.2
    MIP lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] High confidence 1.34524 71386.9 96032.5
    MSI1 Ranked musashi 1. [refseq;acc:nm_002442] 1.14055 227.491 199.458
    NOSTRIN Rooted nostrin. [refseq;acc:nm_052946] 1.1486 59.6399 51.9242
    NOX4 nadph oxidase 4. [refseq;acc:nm_016931] Low confidence 1.06154 69.9166 74.219
    RAF1 Measured raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] High confidence 1.26766 17756.5 14007.3
    STARD7 star-related lipid transfer protein 7 (stard7) (start domain- containing protein 7) (gtt1 protein). [swissprot;acc:q9nqz5] Low confidence 1.07451 6534.34 7021.2
    194 no value Squared transforming protein n-ras. [swissprot;acc:p01111] 1.10846 51474.3 46437.7
    AQP1 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] High confidence 1.34505 71346.6 95965.1
    CCNG2 Measured cyclin g2. [swissprot;acc:q16589] 1.26743 17738.6 13995.7
    COG5 Ranked conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] Low confidence 1.05207 215.723 205.046
    NOX3 Rooted nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] 1.06154 69.9164 74.2188
    SNF8 eap30 subunit of ell complex. [refseq;acc:nm_007241] High confidence 1.1486 59.6399 51.9242
    TMED10 Measured transmembrane protein tmp21 precursor (21 kda transmembrane trafficking protein) (p24delta) (s31iii125) (s31i125) (tmp-21-i). [swissprot;acc:p49755] Low confidence 1.07446 11403 12252.1
    ZC3H14 Ranked nuclear protein ukp68. [refseq;acc:nm_024824] High confidence 1.14055 227.491 199.458
    195 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Low confidence 1.0517 211.679 222.623
    CCNG1 Measured cyclin g1 (cyclin g). [swissprot;acc:p51959] High confidence 1.26743 17738.5 13995.6
    NOX1 Rooted nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] Low confidence 1.06154 69.9166 74.219
    PIGB Measured phosphatidylinositol glycan, class b. [refseq;acc:nm_004855] 1.07446 11403 12252.1
    PRPF40B Ranked huntingtin interacting protein c. [refseq;acc:nm_012272] High confidence 1.13748 227.971 200.417
    SEPT2 Squared septin 2 (nedd5 protein homolog). [swissprot;acc:q15019] Low confidence 1.10833 58865.4 65242.4
    SLC39A6 Rooted liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] High confidence 1.1486 59.6399 51.9242
    SSR4 Squared translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] 1.34373 71062.4 95488.9
    196 ATP1B2 sodium/potassium-transporting atpase beta-2 chain (sodium/potassium- dependent atpase beta-2 subunit). [swissprot;acc:p14415] Low confidence 1.10823 52543.2 47411.7
    CAPZA1 Rooted f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] 1.06149 68.0822 72.2685
    CLSTN1 Squared calsyntenin-1 precursor. [swissprot;acc:o94985] High confidence 1.34373 71062.4 95488.9
    FOXP4 Ranked forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 1.13745 263.215 231.407
    GAD2 Rooted glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] 1.1486 59.6399 51.9242
    GNG12 Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Low confidence 1.0517 211.679 222.623
    PPP2R5E Measured serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] High confidence 1.26742 17738.5 13995.7
    SLC11A2 natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] Low confidence 1.07415 6985.66 7503.62
    197 no value Squared succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] High confidence 1.34373 71062.4 95488.9
    ATP1B4 x/potassium-transporting atpase beta-m chain (x,k-atpase beta-m subunit). [swissprot;acc:q9un42] Low confidence 1.10806 52525.1 47402.9
    DGKH Measured diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] 1.07336 6519.03 6997.26
    FOXP1 Ranked forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] High confidence 1.13745 263.215 231.407
    NAPG Rooted gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] 1.1486 59.6399 51.9242
    PPP2R5A Measured serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] 1.26742 17738.5 13995.7

    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/