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 red Interaction Map Filtered network_comparison green
    Results: HTML CSV LaTeX Showing element 1012 to 1061 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		red
    		network_comparison
    		green
    127 DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Rooted Subtracted 153.191 13.58 166.771
    HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Divided 60.9353 1.23236 75.094
    JUND transcription factor jun-d. [swissprot;acc:p17535] Measured 5638.2 1.33436 7523.39
    MIP lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Squared Subtracted 71386.9 24645.6 96032.5
    RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Measured 450.5 1944 2394.5
    128 no value pnas-18. [sptrembl;acc:q9bzu3] Squared Divided 87787.3 1.50952 58155.8
    AQP1 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Subtracted 71346.6 24618.5 95965.1
    LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Measured Divided 4355.61 1.3341 5810.82
    PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Ranked Subtracted 285.684 33.45 252.234
    STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Divided 94 1.21277 114
    TARDBP tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Rooted 48.0515 1.23069 39.0445
    TCP1 t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Measured Subtracted 11004.2 1940 12944.2
    TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Rooted 54.6527 13.3216 67.9743
    129 CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Ranked 285.684 33.45 252.234
    LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Measured Divided 4358.13 1.33348 5811.49
    NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Rooted 54.2343 1.23044 66.7323
    PCF11 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Squared 178263 1.50257 118639
    PPP1R13B protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Measured Subtracted 15274.9 1928 13346.9
    SSR4 translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Squared 71062.4 24426.5 95488.9
    TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Rooted 54.6625 13.2852 67.9477
    VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Ranked Divided 94 1.21277 114
    130 no value formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Rooted 55.1026 1.22626 67.5701
    C10orf83 44050 protein. [refseq;acc:nm_178832] Squared 148058 1.4861 99628.4
    CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] Ranked 94 1.21277 114
    CLSTN1 calsyntenin-1 precursor. [swissprot;acc:o94985] Squared Subtracted 71062.4 24426.5 95488.9
    EGFL8 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Ranked 242.735 33.324 276.059
    FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Measured Divided 2234.68 1.33287 2978.53
    GATAD2A p66 alpha. [refseq;acc:nm_017660] Subtracted 12839 1927.9 10911.1
    RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Rooted 144.606 13.218 157.824
    131 no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Divided 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
    FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Measured Divided 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
    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] Squared Divided 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
    132 no value tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Measured Subtracted 12839 1927.9 10911.1
    ATG5 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] Squared Divided 36359.2 1.48606 24466.8
    FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Measured 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
    NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Ranked Subtracted 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
    RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Rooted 144.606 13.218 157.824
    TOB2 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Ranked Divided 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
    ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Rooted 144.606 13.218 157.824
    CDK3 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Measured 12798.9 1911.7 10887.2
    GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Divided 23421.5 1.33225 17580.4
    OSR1 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Rooted 45.4558 1.22316 55.5995

    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/