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 Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 2080 to 2129 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		red
    		network_comparison
    		green
    130 TAGLN3 neuronal protein np25. [swissprot;acc:q9ui15] Ranked Subtracted Low confidence 218.66 13.09 205.57
    131 no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Rooted Divided High confidence 55.1113 1.22577 67.5537
    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] Squared Subtracted 71062.4 24426.5 95488.9
    EGFL7 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Ranked 242.718 33.3 276.018
    F13A1 coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] Rooted Divided Low confidence 63.8063 1.07324 68.4797
    FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Measured High confidence 2234.73 1.33285 2978.57
    GATAD2B transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Subtracted 12839 1927.9 10911.1
    GTF3A transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Low confidence 7624.8 767.05 8391.85
    NHLH2 helix-loop-helix protein 2 (hen2) (nescient helix loop helix 2) (nscl- 2). [swissprot;acc:q02577] Squared Divided 55864.7 1.13547 49199.8
    PPP1R7 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Subtracted 60231.9 7091.2 53140.7
    PPP1R8 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] Divided High confidence 148058 1.4861 99628.4
    RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Rooted Subtracted 144.606 13.218 157.824
    SON 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] Ranked Divided 294.053 1.21228 242.562
    STRN4 striatin 4 (zinedin). [swissprot;acc:q9nrl3] Low confidence 213.878 1.065 200.825
    Subtracted 13.053
    TRO trophinin. [swissprot;acc:q12816] Measured Divided 11285.3 1.0937 10318.5
    VPS41 vacuolar assembly protein vps41 homolog (s53). [swissprot;acc:p49754] Rooted Subtracted 70.0842 5.2785 75.3627
    132 no value tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Measured High confidence 12839 1927.9 10911.1
    ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Rooted Low confidence 100.524 5.2525 95.2715
    ATG5 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] Squared Divided High confidence 36359.2 1.48606 24466.8
    DAZAP1 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Ranked Low confidence 220.268 1.06411 206.997
    DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Measured Subtracted 7030.67 764.13 7794.8
    Ranked 203.016 13.051 189.965
    FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Measured Divided High confidence 2236.61 1.33253 2980.35
    HAT1 histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Rooted 44.963 1.22451 55.0576
    HPRT1 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Squared Low confidence 65137.2 1.13524 73946.3
    MAP2K4 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] Measured 5948.88 1.09318 5441.83
    NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Ranked Subtracted High confidence 229.406 32.711 196.695
    PTPRB protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Squared 71062.2 24426.4 95488.6
    RBM10 rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] Low confidence 67930.9 6984.3 60946.6
    RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Rooted High confidence 144.606 13.218 157.824
    TGM1 protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] Divided Low confidence 63.8063 1.07324 68.4797
    TOB2 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Ranked High confidence 350 1.2069 290
    133 no value formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Subtracted 226.887 32.167 194.72
    ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Measured Divided Low confidence 7013 1.09265 7662.77
    ABRA striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] Rooted 65.2217 1.07261 69.9574
    ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Subtracted High confidence 144.606 13.218 157.824
    BBS9 pth-responsive osteosarcoma b1 protein. [refseq;acc:nm_014451] Squared Divided Low confidence 55849.9 1.13517 49199.6
    CDK3 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Measured Subtracted High confidence 12798.9 1911.7 10887.2
    DVL2 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Low confidence 7034.43 762.71 7797.14
    Ranked 203.007 13.022 189.985
    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] Rooted 64.712 5.1695 69.8815
    GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Measured Divided High confidence 23421.5 1.33225 17580.4
    INADL inad-like protein isoform 3; pdz domain protein (drosophila inad-like); protein associated to tight junctions; pals1-associated tight junction protein; inactivation no after-potential d-like protein. [refseq;acc:nm_005799] Squared Subtracted Low confidence 67882.7 6969 60913.7
    OSR1 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Rooted Divided High confidence 45.4558 1.22316 55.5995
    PROM1 prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Ranked Low confidence 220.268 1.06411 206.997
    PRSS16 thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Squared Subtracted High confidence 71062.2 24426.4 95488.6
    TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] Divided 1182.25 1.46039 1726.55
    TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Ranked 350 1.2069 290
    134 no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Measured 21785.2 1.32626 16426.1

    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/