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 description Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 5358 to 5407 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		network_comparison
    		green
    2679 C13orf1 clll6 protein. [refseq;acc:nm_020456] Low confidence 203.566 1.01762 200.041
    2680 HRAS transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] High confidence 144.422 1.00096 144.56
    TMEM147 seven transmembrane domain protein. [refseq;acc:nm_032635] Low confidence 208.542 1.01762 212.217
    2681 OTUB2 ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112] High confidence 203.592 1.00096 203.787
    TMED10 transmembrane protein tmp21 precursor (21 kda transmembrane trafficking protein) (p24delta) (s31iii125) (s31i125) (tmp-21-i). [swissprot;acc:p49755] Low confidence 182.789 1.01761 179.625
    2682 no value transforming protein n-ras. [swissprot;acc:p01111] High confidence 144.427 1.00095 144.564
    SUPV3L1 suppressor of var1, 3-like 1. [refseq;acc:nm_003171] Low confidence 200.492 1.01761 197.022
    2683 DCLK1 serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] 201.045 197.566
    YBX1 nuclease sensitive element binding protein 1 (y box binding protein-1) (y-box transcription factor) (yb-1) (ccaat-binding transcription factor i subunit a) (cbf-a) (enhancer factor i subunit a) (efi-a) (dna-binding protein b) (dbpb). [swissprot;acc:p16991] High confidence 208.438 1.00095 208.635
    2684 CSDA dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989]
    PFDN5 prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] Low confidence 200.242 1.01761 196.776
    2685 PIGB phosphatidylinositol glycan, class b. [refseq;acc:nm_004855] 182.789 179.625
    YBX2 germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982] High confidence 208.438 1.00095 208.635
    2686 PSMB7 proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [swissprot;acc:q99436] 219.829 1.00091 219.629
    STIP1 stress-induced-phosphoprotein 1 (sti1) (hsp70/hsp90-organizing protein) (transformation-sensitive protein ief ssp 3521). [swissprot;acc:p31948] Low confidence 197.695 1.0176 194.276
    2687 BCAT2 branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] High confidence 210.939 1.00087 210.755
    ERCC3 tfiih basal transcription factor complex helicase xpb subunit (ec 3.6.1.-) (basic transcription factor 2 89 kda subunit) (btf2-p89) (tfiih 89 kda subunit) (dna-repair protein complementing xp-b cells) (xeroderma pigmentosum group b complementing protein) (dna excision repair protein ercc-3). [swissprot;acc:p19447] Low confidence 197.695 1.0176 194.276
    2688 no value peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] High confidence 194.557 1.00085 194.392
    AARS alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] Low confidence 201.799 1.0176 198.308
    2689 ACLY atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396] High confidence 213.792 1.00081 213.619
    CRISP1 cysteine-rich secretory protein-1 precursor (crisp-1) (acidic epididymal glycoprotein homolog) (aeg-like protein) (arp). [swissprot;acc:p54107] Low confidence 205.763 1.01759 202.207
    2690 AQP4 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] High confidence 188.191 1.00077 188.046
    CRISP2 testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] Low confidence 205.763 1.01759 202.207
    2691 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 188.193 1.00077 188.048
    PEX14 peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] Low confidence 201.441 1.01758 197.96
    2692 AQP5 aquaporin 5. [swissprot;acc:p55064] High confidence 188.192 1.00077 188.048
    EIF2B4 translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10] Low confidence 202.466 1.01758 198.969
    2693 DDX43 dead-box protein. [refseq;acc:nm_018665] 202.135 198.643
    MIP lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] High confidence 188.193 1.00077 188.049
    2694 AQP1 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] 188.223 1.00075 188.081
    BYSL bystin. [swissprot;acc:q13895] Low confidence 200.546 1.01757 197.084
    2695 no value prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212] 196.216 192.828
    SRP54 signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624] High confidence 215.545 1.00075 215.384
    2696 no value 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] Low confidence 196.941 1.01757 193.541
    ACO1 iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:p21399] High confidence 201.652 1.0007 201.794
    2697 no value suppressor of actin 1. [refseq;acc:nm_014016] Low confidence 200.82 1.01756 197.354
    ARPC2 arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144] High confidence 225.081 1.00067 225.232
    2698 ETNK1 ethanolamine kinase (ec 2.7.1.82) (eki). [swissprot;acc:q9hbu6] Low confidence 200.085 1.01756 196.633
    SSR4 translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] High confidence 188.435 1.00066 188.31
    2699 no value ataxin 2-binding protein. [swissprot;acc:q9nwb1] Low confidence 203.718 1.01756 200.202
    CLSTN1 calsyntenin-1 precursor. [swissprot;acc:o94985] High confidence 188.435 1.00066 188.31
    2700 no value 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]
    ZFYVE19 zinc finger, fyve domain containing 19. [refseq;acc:nm_032850] Low confidence 208.568 1.01755 204.97
    2701 CAMK4 calcium/calmodulin-dependent protein kinase type iv catalytic chain (ec 2.7.1.123) (cam kinase-gr) (camk iv). [swissprot;acc:q16566] 197.047 193.649
    DCLK1 serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] High confidence 216.539 1.00066 216.682
    2702 PTPRB protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] 188.435 188.311
    RNGTT mrna capping enzyme (hce) (hcap1) [includes: polynucleotide 5'- triphosphatase (ec 3.1.3.33) (mrna 5'-triphosphatase) (tpase); mrna guanylyltransferase (ec 2.7.7.50) (gtp--rna guanylyltransferase) (gtase)]. [swissprot;acc:o60942] Low confidence 203.877 1.01755 200.361
    2703 MRPL27 mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] 206.23 202.673
    PRSS16 thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] High confidence 188.435 1.00066 188.311
    2704 ARFGAP1 adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3] Low confidence 199.109 1.01755 195.675

    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/