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 green network_comparison
    Results: HTML CSV LaTeX Showing element 3375 to 3424 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    844 MOBKL3 preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Measured 6276.97 6934.8 1.1048
    TULP3 tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Rooted 65.0565 69.1533 1.06297
    845 DNAJB11 dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4] Measured 6276.97 6934.8 1.1048
    LSM1 u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Ranked 228.599 219.399 1.04193
    STARD5 star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2] Squared 31100.1 36086.4 1.16033
    VPS35 vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Rooted 65.0565 69.1533 1.06297
    846 no value methyltransferase like 2. [refseq;acc:nm_018396] Ranked 147.211 153.371 1.04184
    HLCS biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] Measured 5607.43 6194.98 1.10478
    KRTAP4-4 keratin associated protein 4.4. [refseq;acc:nm_032524] Squared 31100.2 36086.5 1.16033
    PRKCZ protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Rooted 65.0565 69.1533 1.06297
    847 no value alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] Squared 31100.1 36086.4 1.16033
    DYNLT1 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Ranked 147.211 153.371 1.04184
    NCK2 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] Measured 6776.85 7485.55 1.10458
    WDR46 wd-repeat protein bing4. [swissprot;acc:o15213] Rooted 51.7527 55.0117 1.06297
    848 FZR1 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Ranked 147.211 153.371 1.04184
    HEATR1 protein bap28. [swissprot;acc:q9h583] Rooted 51.1817 54.4034 1.06295
    LIMS1 pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059] Squared 31100.1 36086.4 1.16033
    WDR46 wd-repeat protein bing4. [swissprot;acc:o15213] Measured 4066.56 4491.65 1.10453
    849 DDB1 dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] 6194.15 6839.37 1.10417
    ILK integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418] Squared 31100.1 36086.4 1.16033
    PCSK5 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Ranked 147.211 153.371 1.04184
    RRS1 ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Rooted 124.41 117.043 1.06294
    850 CPSF4 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Ranked 107.842 112.329 1.04161
    PCCB propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] Measured 6194.15 6839.37 1.10417
    PPP1CA serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Rooted 124.41 117.043 1.06294
    STARD4 star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4] Squared 31100.1 36086.4 1.16033
    851 ATP2C2 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Rooted 65.1512 69.252 1.06294
    CSNK2A1P casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] Measured 4307.12 4755.03 1.10399
    KIAA1012 trs85 homolog. [swissprot;acc:q9y2l5] Ranked 107.842 112.329 1.04161
    RSU1 ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404] Squared 31100.1 36086.4 1.16033
    852 CSNK2A2 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] Measured 4307.12 4755.03 1.10399
    G3BP1 ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283] Squared 31100.1 36086.4 1.16033
    HPRT1 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Ranked 193.114 185.412 1.04154
    MTRF1 peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Rooted 58.5869 62.2732 1.06292
    853 AATF apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] Measured 4078.45 4502.32 1.10393
    G3BP2 ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86] Squared 31100.1 36086.4 1.16033
    TOE1 target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Rooted 64.0287 68.0566 1.06291
    WDR33 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Ranked 108.289 112.772 1.0414
    854 no value keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] Squared 31100.2 36086.5 1.16033
    uba/ubx 33.3 kda protein. [swissprot;acc:q04323] Measured 6562.98 7242.37 1.10352
    CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Ranked 108.289 112.772 1.0414
    KPNA3 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] Rooted 64.0316 68.0597 1.06291
    855 no value ero1-like. [refseq;acc:nm_014584] Measured 6562.98 7242.37 1.10352
    CLEC3B tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Ranked 178.514 171.42 1.04138
    ESPNP espin. [refseq;acc:nm_031475] Squared 31100.1 36086.4 1.16033
    KPNA4 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Rooted 64.0262 68.0537 1.0629
    856 CYP2D6 cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635] Squared 31100.1 36086.4 1.16033
    MPDU1 mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] Rooted 58.5944 62.2766 1.06284
    NDST2 heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849] Measured 5210.58 5749.33 1.1034
    XPR1 xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Ranked 215.028 206.623 1.04068

    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/