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 6408 to 6457 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    1602 PMM1 phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Divided High confidence 217.334 213.914 1.01599
    1603 no value heat shock factor binding protein 1. [swissprot;acc:o75506] 216.62 213.22 1.01595
    CLPP putative atp-dependent clp protease proteolytic subunit, mitochondrial precursor (ec 3.4.21.92) (endopeptidase clp). [swissprot;acc:q16740] Low confidence 204.216 200.037 1.02089
    EEA1 early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566] Subtracted High confidence 228.654 231.933 3.279
    SEPT8 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Low confidence 152.572 148.47 4.102
    1604 ATG5 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] Divided 204.216 200.037 1.02089
    BUB3 mitotic checkpoint protein bub3. [swissprot;acc:o43684] Subtracted High confidence 221.934 218.658 3.276
    CLK2 protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] Divided 214.984 211.614 1.01593
    IKBKE inhibitor of nuclear factor kappa-b kinase epsilon subunit (ec 2.7.1.-) (i kappa-b kinase epsilon) (ikbke) (ikk-epsilon) (ikk-e) (inducible i kappa-b kinase) (ikk-i). [swissprot;acc:q14164] Subtracted Low confidence 204.39 200.288 4.102
    1605 DUSP15 dual specificity protein phosphatase 15 (ec 3.1.3.48) (ec 3.1.3.16). [swissprot;acc:q9h1r2] Divided 199.691 195.607 1.02088
    FOXA1 hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] High confidence 217.322 213.916 1.01592
    NARS asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776] Subtracted Low confidence 201.291 197.189 4.102
    ZNF207 zinc finger protein 207. [swissprot;acc:o43670] High confidence 221.934 218.658 3.276
    1606 APOA1BP apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Divided 207.916 204.662 1.0159
    CCDC85B delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] Subtracted Low confidence 201.993 197.894 4.099
    MORF4L2 transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [swissprot;acc:q15014] High confidence 228.477 231.747 3.27
    POLE3 dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] Divided Low confidence 204.475 200.292 1.02088
    1607 no value transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] Subtracted High confidence 228.484 231.74 3.256
    CLK3 protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Divided 214.982 211.622 1.01588
    DUSP5 dual specificity protein phosphatase 5 (ec 3.1.3.48) (ec 3.1.3.16) (dual specificity protein phosphatase hvh3). [swissprot;acc:q16690] Low confidence 199.691 195.607 1.02088
    TKT transketolase (ec 2.2.1.1) (tk). [swissprot;acc:p29401] Subtracted 201.817 197.718 4.099
    1608 ADSL adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] Divided 199.691 195.607 1.02088
    CHTF18 ctf18, chromosome transmission fidelity factor 18 homolog; homolog of yeast chl12. [refseq;acc:nm_022092] Subtracted 200.714 196.617 4.097
    GSPT1 g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] High confidence 218.789 215.533 3.256
    TMEM189 ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] Divided 208.106 204.867 1.01581
    1609 APOA1BP apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Subtracted 207.916 204.662 3.254
    DUSP13 dual specificity protein phosphatase 13 (ec 3.1.3.48) (ec 3.1.3.16) (testis- and skeletal-muscle-specific dsp). [swissprot;acc:q9uii6] Divided Low confidence 199.691 195.607 1.02088
    HOXC8 homeobox protein hox-c8 (hox-3a). [swissprot;acc:p31273] Subtracted 203.127 199.033 4.094
    UGP2 utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Divided High confidence 208.113 204.876 1.0158
    1610 MUS81 mus81 endonuclease. [refseq;acc:nm_025128] Low confidence 195.31 191.317 1.02087
    PBLD mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] Subtracted 185.205 181.112 4.093
    RPUSD2 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] High confidence 217.446 214.2 3.246
    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] Divided 208.122 204.886 1.01579
    1611 CEP70 p10-binding protein. [refseq;acc:nm_024491] 221.313 217.877 1.01577
    FAM119A similar to hepatocellular carcinoma-associated antigen hca557b. [refseq;acc:nm_145280] Low confidence 195.31 191.317 1.02087
    HAS2 hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819] Subtracted 197.747 193.656 4.091
    TMBIM4 z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] High confidence 217.446 214.2 3.246
    1612 no value enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] Divided 221.426 224.902 1.0157
    FAM119B hepatocellularcarcinoma-associated antigen hca557a. [refseq;acc:nm_015433] Low confidence 195.31 191.317 1.02087
    HAS1 hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] Subtracted 197.752 193.661 4.091
    TMBIM1 pp1201 protein. [refseq;acc:nm_022152] High confidence 217.446 214.2 3.246
    1613 FAIM2 lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]
    GTPBP3 mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] Divided Low confidence 192.787 188.847 1.02086
    HAS3 hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219] Subtracted 197.74 193.65 4.09
    HTATIP2 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] Divided High confidence 182.378 185.241 1.0157
    1614 no value sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Subtracted 217.446 214.2 3.246
    FOXA2 hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] Divided 217.233 213.897 1.0156
    RAP2B ras-related protein rap-2b. [swissprot;acc:p17964] Low confidence 202.026 197.9 1.02085
    ZNF622 zinc finger-like protein 9. [refseq;acc:nm_033414] Subtracted 202.494 198.406 4.088
    1615 CXXC1 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] Divided 205.179 200.988 1.02085

    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/