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 Value Type Hugo description Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 1501 to 1550 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		Hugo
    		description
    		Interaction Map
    		network_comparison
    		red
    		green
    188 Squared HS3ST2 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] High confidence 1.34589 41502.9 30836.8
    KRAS transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Low confidence 1.10966 51551.5 46457.1
    Rooted DUOX1 dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] 1.06171 69.8912 74.2044
    E2F1 transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] High confidence 1.15171 46.0352 53.0192
    189 Measured SLC11A1 natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] Low confidence 1.0754 6933.47 7456.24
    STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] High confidence 1.28281 4571.89 5864.86
    Ranked DNALI1 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Low confidence 1.05264 214.779 204.039
    PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] High confidence 1.14179 226.582 198.444
    Squared CENPJ centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] Low confidence 1.10919 65169.1 58753.9
    DCPS mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] High confidence 1.34589 41502.9 30836.8
    Rooted DGAT1 diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] Low confidence 1.06161 69.9065 74.2132
    E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] High confidence 1.15171 46.0352 53.0192
    190 Measured DDOST 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] 1.28281 4571.89 5864.86
    TFDP2 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Low confidence 1.07485 6480.93 6966.05
    Ranked FMO5 dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] 1.0524 210.557 200.074
    SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] High confidence 1.14179 226.582 198.444
    Squared no value ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Low confidence 1.10898 51507.8 46446.1
    AQP4 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] High confidence 1.34525 71389.9 96037.6
    Rooted FMO5 dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] Low confidence 1.06159 69.0062 73.256
    GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] High confidence 1.15009 149.165 129.699
    191 Measured AGBL3 similar to atp/gtp-binding protein. [sptrembl;acc:q8nem8] Low confidence 1.07469 9385.4 10086.4
    SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] High confidence 1.27712 4638.1 5923.4
    Ranked no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 1.14179 226.582 198.444
    SLC15A2 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
    Squared AQP5 aquaporin 5. [swissprot;acc:p55064] High confidence 1.34525 71388.5 96035.2
    ICK intestinal cell kinase isoform a; mak-related kinase; serine/threonine protein kinase. [refseq;acc:nm_014920] Low confidence 1.10897 45402.8 50350.5
    Rooted CYBB cytochrome b-245 heavy chain (p22 phagocyte b-cytochrome) (neutrophil cytochrome b, 91 kda polypeptide) (cgd91-phox) (gp91-phox) (heme binding membrane glycoprotein gp91phox) (cytochrome b(558) beta chain) (superoxide-generating nadph oxidase heavy chain subunit). [swissprot;acc:p04839] 1.06154 69.9165 74.2189
    PLDN pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] High confidence 1.14995 63.1192 72.584
    192 Measured ARAF 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
    TRMU trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Low confidence 1.07469 9385.4 10086.4
    Ranked MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] High confidence 1.14055 227.491 199.458
    RC3H2 membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] Low confidence 1.05214 217.341 206.571
    Squared AQP2 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
    SHOC2 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Low confidence 1.10896 51506.6 46445.8
    Rooted NOX5 nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] 1.06154 69.9161 74.2187
    SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] High confidence 1.14877 53.6107 61.5862
    193 Measured RAF1 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] 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
    Ranked HBS1L hbs1-like. [refseq;acc:nm_006620] 1.05213 206.166 216.913
    MSI1 musashi 1. [refseq;acc:nm_002442] High confidence 1.14055 227.491 199.458
    Squared HRAS transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Low confidence 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
    Rooted NOSTRIN 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
    194 Measured CCNG2 cyclin g2. [swissprot;acc:q16589] High confidence 1.26743 17738.6 13995.7
    TMED10 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
    Ranked COG5 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] 1.05207 215.723 205.046
    ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] High confidence 1.14055 227.491 199.458
    Squared no value transforming protein n-ras. [swissprot;acc:p01111] Low confidence 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

    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/