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 Hugo Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 12864 to 12913 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		description
    		Value Type
    		red
    		green
    		network_comparison
    1608 UBC Divided ubiquitin. [swissprot;acc:p02248] Measured 6158.22 6597.55 1.07134
    1609 APOA1BP Subtracted apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Ranked 207.916 204.662 3.254
    DCLK1 serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] Measured 6297.05 6721.08 424.03
    EIF2S3 eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] Squared 24291.6 26802.4 2510.8
    PSMB5 Divided proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [swissprot;acc:p28074] Rooted 65.5919 67.884 1.03494
    PSMD10 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] Measured 5826.74 6242.44 1.07134
    SALL4 Subtracted sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Rooted 61.9701 64.1935 2.2234
    UGP2 Divided utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Ranked 208.113 204.876 1.0158
    WTAP wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007] Squared 28992.5 32145.6 1.10876
    1610 EIF5A2 eif-5a2 protein. [refseq;acc:nm_020390] Measured 6222.4 6665.83 1.07126
    FES Subtracted proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] 6079.19 6503.12 423.93
    KRR1 Divided hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] Squared 15639.2 17338.5 1.10866
    RPUSD2 Subtracted c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Ranked 217.446 214.2 3.246
    SLC5A5 Divided sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Rooted 67.4766 69.831 1.03489
    SNAP91 Subtracted clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] 61.9701 64.1935 2.2234
    TMF1 tata element modulatory factor (tmf). [swissprot;acc:p82094] Squared 23713.7 26223.8 2510.1
    UBE2V2 Divided ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] Ranked 208.122 204.886 1.01579
    1611 no value heat shock factor binding protein 1. [swissprot;acc:o75506] Squared 27263.5 30225.7 1.10865
    CEP70 p10-binding protein. [refseq;acc:nm_024491] Ranked 221.313 217.877 1.01577
    MOCS2 Subtracted molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007] Measured 6079.19 6503.12 423.93
    PRODH2 Divided kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Rooted 67.4958 69.8487 1.03486
    RERE Subtracted arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102] 61.9705 64.1938 2.2233
    SCYL1 scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680] Squared 23713.7 26223.8 2510.1
    TMBIM4 z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Ranked 217.446 214.2 3.246
    TRIP10 Divided cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] Measured 5497.73 5132.35 1.07119
    1612 no value brain protein 16. [refseq;acc:nm_016458] Squared 26202.2 29043.8 1.10845
    enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] Ranked 221.426 224.902 1.0157
    ANAPC10 Subtracted anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Measured 6079.19 6503.12 423.93
    EIF5AP1 Divided eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159] 6212.98 6655.12 1.07116
    NUP98 Subtracted nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] Squared 23713.7 26223.8 2510.1
    SLC5A8 Divided solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] Rooted 67.5045 69.8568 1.03485
    TMBIM1 Subtracted pp1201 protein. [refseq;acc:nm_022152] Ranked 217.446 214.2 3.246
    USP8 ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818] Rooted 61.9703 64.1936 2.2233
    1613 AMMECR1 ammecr1 protein. [refseq;acc:nm_015365] Squared 23713.7 26223.8 2510.1
    FAIM2 lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Ranked 217.446 214.2 3.246
    HTATIP2 Divided hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [refseq;acc:nm_006410] 182.378 185.241 1.0157
    MRPS22 mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] Measured 6035.6 6464.5 1.07106
    NETO2 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] Squared 15399.5 17067.9 1.10834
    ROD1 Subtracted rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [refseq;acc:nm_005156] Rooted 61.9703 64.1936 2.2233
    RPL29 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] Measured 6079.19 6503.12 423.93
    SLC5A6 Divided sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] Rooted 67.511 69.8628 1.03484
    1614 no value nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946] Measured 6035.6 6464.5 1.07106
    Subtracted sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Ranked 217.446 214.2 3.246
    FER proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Measured 6079.19 6503.12 423.93
    FOXA2 Divided hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] Ranked 217.233 213.897 1.0156
    NETO1 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] Squared 15399.5 17067.9 1.10834
    PDSS1 trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Rooted 54.1932 56.0802 1.03482
    PTBP2 Subtracted polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190] 61.9703 64.1936 2.2233
    RAE1 mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] Squared 23713.7 26223.8 2510.1
    1615 AAK1 adaptor-associated kinase 1. [refseq;acc:nm_014911] Rooted 61.9703 64.1936 2.2233

    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/