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 description Hugo Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 2062 to 2111 of 66312 in total
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    129 retinoblastoma-associated factor 600. [refseq;acc:nm_020765] UBR4 Squared Subtracted Low confidence 27909.1 35068.7 7159.6
    transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] TAGLN Ranked 218.561 205.431 13.13
    translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] SSR4 Squared High confidence 71062.4 95488.9 24426.5
    130 44050 protein. [refseq;acc:nm_178832] C10orf83 Divided 148058 99628.4 1.4861
    calsyntenin-1 precursor. [swissprot;acc:o94985] CLSTN1 Subtracted 71062.4 95488.9 24426.5
    defender against cell death 1 (dad-1). [swissprot;acc:p46966] DAD1 Rooted Divided Low confidence 69.1344 74.2065 1.07337
    forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] FOXP4 Measured High confidence 2234.68 2978.53 1.33287
    formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] no value Rooted 55.1026 67.5701 1.22626
    melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] MAGED2 Measured Low confidence 11285.3 10318.5 1.0937
    neuronal protein np25. [swissprot;acc:q9ui15] TAGLN3 Ranked Subtracted 218.66 205.57 13.09
    p66 alpha. [refseq;acc:nm_017660] GATAD2A Measured High confidence 12839 10911.1 1927.9
    palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] EGFL8 Ranked 242.735 276.059 33.324
    presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] PSEN1 Rooted Low confidence 66.9562 72.3243 5.3681
    protein hspc134 (protein cda04). [swissprot;acc:q9by43] CHMP4A Ranked Divided High confidence 94 114 1.21277
    protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] PRKRAP1 Measured Subtracted Low confidence 3840.85 4614.87 774.02
    ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] RRAGA Squared Divided 56706.1 64418 1.136
    Rooted Subtracted High confidence 144.606 157.824 13.218
    rho guanine nucleotide exchange factor 5 (guanine nucleotide regulatory protein tim) (oncogene tim) (p60 tim) (transforming immortalized mammary oncogene). [swissprot;acc:q12774] ARHGEF5 Squared Low confidence 58231.9 51117.1 7114.8
    striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] ABRA Ranked Divided 225.495 211.529 1.06602
    131 coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] F13A1 Rooted 63.8063 68.4797 1.07324
    egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] EGFL7 Ranked Subtracted High confidence 242.718 276.018 33.3
    forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] FOXP1 Measured Divided 2234.73 2978.57 1.33285
    helix-loop-helix protein 2 (hen2) (nescient helix loop helix 2) (nscl- 2). [swissprot;acc:q02577] NHLH2 Squared Low confidence 55864.7 49199.8 1.13547
    huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] no value Rooted High confidence 55.1113 67.5537 1.22577
    nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] PPP1R8 Squared 148058 99628.4 1.4861
    protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] PPP1R7 Subtracted Low confidence 60231.9 53140.7 7091.2
    ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] RRAGC Rooted High confidence 144.606 157.824 13.218
    son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] SON Ranked Divided 294.053 242.562 1.21228
    striatin 4 (zinedin). [swissprot;acc:q9nrl3] STRN4 Low confidence 213.878 200.825 1.065
    Subtracted 13.053
    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] no value Squared High confidence 71062.4 95488.9 24426.5
    transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] GTF3A Measured Low confidence 7624.8 8391.85 767.05
    transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] GATAD2B High confidence 12839 10911.1 1927.9
    trophinin. [swissprot;acc:q12816] TRO Divided Low confidence 11285.3 10318.5 1.0937
    vacuolar assembly protein vps41 homolog (s53). [swissprot;acc:p49754] VPS41 Rooted Subtracted 70.0842 75.3627 5.2785
    132 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] ATG5 Squared Divided High confidence 36359.2 24466.8 1.48606
    cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] ATG4A Rooted Subtracted Low confidence 100.524 95.2715 5.2525
    daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] DAZAP1 Ranked Divided 220.268 206.997 1.06411
    dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] NCBP2L Subtracted High confidence 229.406 196.695 32.711
    dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] MAP2K4 Measured Divided Low confidence 5948.88 5441.83 1.09318
    forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] FOXP3 High confidence 2236.61 2980.35 1.33253
    histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] HAT1 Rooted 44.963 55.0576 1.22451
    hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] HPRT1 Squared Low confidence 65137.2 73946.3 1.13524
    protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] TGM1 Rooted 63.8063 68.4797 1.07324
    protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] PTPRB Squared Subtracted High confidence 71062.2 95488.6 24426.4
    ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] RRAGB Rooted 144.606 157.824 13.218
    rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] RBM10 Squared Low confidence 67930.9 60946.6 6984.3
    segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] DVL1 Measured 7030.67 7794.8 764.13
    Ranked 203.016 189.965 13.051
    tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] TOB2 Divided High confidence 350 290 1.2069

    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/