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 green network_comparison
    Results: HTML CSV LaTeX Showing element 1801 to 1850 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    451 no value small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Squared 17543.3 21222.5 1.20972
    MRPL17 mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Rooted 50.268 45.8663 1.09597
    MYCN n-myc proto-oncogene protein. [swissprot;acc:p04198] Measured 4889.71 5610.69 1.14745
    POLR3C polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Ranked 239.092 257.705 1.07785
    452 no value adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Rooted 50.4595 46.0415 1.09596
    ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Ranked 224.161 207.972 1.07784
    SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Squared 17543.3 21222.5 1.20972
    ZNF622 zinc finger-like protein 9. [refseq;acc:nm_033414] Measured 3760.8 4315.06 1.14738
    453 MED22 surfeit locus protein 5. [swissprot;acc:q15528] Rooted 50.4595 46.0413 1.09596
    PPP6C serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] Squared 31620.5 38250.7 1.20968
    SLC45A2 membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] Measured 3760.8 4315.06 1.14738
    SNRPA1 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Ranked 224.161 207.972 1.07784
    454 no value 40s ribosomal protein s26. [swissprot;acc:p02383] 210.224 226.578 1.07779
    guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Measured 3760.8 4315.06 1.14738
    AK3 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] Rooted 50.4595 46.0412 1.09596
    SAPS3 sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] Squared 31620.5 38250.7 1.20968
    455 ACACA acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] 31597.8 38216.9 1.20948
    GABPA ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Measured 4890.51 5610.95 1.14731
    SCAPER zinc finger protein 291. [swissprot;acc:q9by12] Rooted 50.4595 46.0413 1.09596
    TIMM22 mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Ranked 210.225 226.578 1.07779
    456 no value ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Measured 4890.51 5610.95 1.14731
    ATPAF2 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] Ranked 210.225 226.578 1.07779
    NXF5 nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Squared 10933.6 13219.6 1.20908
    PEX1 peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] Rooted 50.4595 46.0413 1.09596
    457 NDUFS8 nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Measured 4890.51 5610.95 1.14731
    NXF3 nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Squared 10936.1 13221.9 1.20901
    TXNDC9 protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Rooted 50.4595 46.0413 1.09596
    UQCRB ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] Ranked 210.225 226.578 1.07779
    458 ELOVL1 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] Measured 4890.55 5610.96 1.14731
    MRPL36 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Rooted 50.2954 45.9216 1.09524
    NXF1 nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Squared 10950.4 13235.9 1.20871
    SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Ranked 235.922 218.925 1.07764
    459 BAG3 bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] 233.529 216.737 1.07748
    MYC myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Measured 4892.16 5611.48 1.14704
    PEF1 pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Squared 27096.7 32743.5 1.20839
    VAV1 vav proto-oncogene. [swissprot;acc:p15498] Rooted 66.0892 72.3741 1.0951
    460 PRMT3 protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] 50.6156 46.2239 1.09501
    RRP1 nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Measured 3790.11 4346.98 1.14693
    SF3A2 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Ranked 223.648 207.62 1.0772
    TMEM189 ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] Squared 29547.4 35683.5 1.20767
    461 no value 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] Rooted 50.6156 46.2239 1.09501
    GRAP grb2-related adaptor protein. [swissprot;acc:q13588] Measured 5986.65 6865.68 1.14683
    KLF5 krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Ranked 223.648 207.62 1.0772
    UGP2 utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Squared 29544.1 35678.3 1.20763
    462 no value ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Measured 11383.2 9926.61 1.14674
    MKI67IP mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Ranked 254.434 236.224 1.07709
    RPS3 40s ribosomal protein s3. [swissprot;acc:p23396] Rooted 50.6274 46.236 1.09498
    UBE2V2 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] Squared 29540.4 35672.6 1.20759
    463 AKT1 rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Rooted 50.2317 55.0025 1.09498
    ATP2C1 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Squared 25533.3 30810.8 1.20669

    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/