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 network_comparison green
    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
    		network_comparison
    		green
    1602 PMM1 phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Divided High confidence 217.334 1.01599 213.914
    1603 no value heat shock factor binding protein 1. [swissprot;acc:o75506] 216.62 1.01595 213.22
    CLPP putative atp-dependent clp protease proteolytic subunit, mitochondrial precursor (ec 3.4.21.92) (endopeptidase clp). [swissprot;acc:q16740] Low confidence 204.216 1.02089 200.037
    EEA1 early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566] Subtracted High confidence 228.654 3.279 231.933
    SEPT8 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Low confidence 152.572 4.102 148.47
    1604 ATG5 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] Divided 204.216 1.02089 200.037
    BUB3 mitotic checkpoint protein bub3. [swissprot;acc:o43684] Subtracted High confidence 221.934 3.276 218.658
    CLK2 protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] Divided 214.984 1.01593 211.614
    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 4.102 200.288
    1605 DUSP15 dual specificity protein phosphatase 15 (ec 3.1.3.48) (ec 3.1.3.16). [swissprot;acc:q9h1r2] Divided 199.691 1.02088 195.607
    FOXA1 hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] High confidence 217.322 1.01592 213.916
    NARS asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776] Subtracted Low confidence 201.291 4.102 197.189
    ZNF207 zinc finger protein 207. [swissprot;acc:o43670] High confidence 221.934 3.276 218.658
    1606 APOA1BP apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Divided 207.916 1.0159 204.662
    CCDC85B delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] Subtracted Low confidence 201.993 4.099 197.894
    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 3.27 231.747
    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 1.02088 200.292
    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 3.256 231.74
    CLK3 protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Divided 214.982 1.01588 211.622
    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 1.02088 195.607
    TKT transketolase (ec 2.2.1.1) (tk). [swissprot;acc:p29401] Subtracted 201.817 4.099 197.718
    1608 ADSL adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] Divided 199.691 1.02088 195.607
    CHTF18 ctf18, chromosome transmission fidelity factor 18 homolog; homolog of yeast chl12. [refseq;acc:nm_022092] Subtracted 200.714 4.097 196.617
    GSPT1 g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] High confidence 218.789 3.256 215.533
    TMEM189 ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] Divided 208.106 1.01581 204.867
    1609 APOA1BP apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Subtracted 207.916 3.254 204.662
    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 1.02088 195.607
    HOXC8 homeobox protein hox-c8 (hox-3a). [swissprot;acc:p31273] Subtracted 203.127 4.094 199.033
    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 1.0158 204.876
    1610 MUS81 mus81 endonuclease. [refseq;acc:nm_025128] Low confidence 195.31 1.02087 191.317
    PBLD mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] Subtracted 185.205 4.093 181.112
    RPUSD2 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] High confidence 217.446 3.246 214.2
    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 1.01579 204.886
    1611 CEP70 p10-binding protein. [refseq;acc:nm_024491] 221.313 1.01577 217.877
    FAM119A similar to hepatocellular carcinoma-associated antigen hca557b. [refseq;acc:nm_145280] Low confidence 195.31 1.02087 191.317
    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 4.091 193.656
    TMBIM4 z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] High confidence 217.446 3.246 214.2
    1612 no value enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] Divided 221.426 1.0157 224.902
    FAM119B hepatocellularcarcinoma-associated antigen hca557a. [refseq;acc:nm_015433] Low confidence 195.31 1.02087 191.317
    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 4.091 193.661
    TMBIM1 pp1201 protein. [refseq;acc:nm_022152] High confidence 217.446 3.246 214.2
    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 1.02086 188.847
    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 4.09 193.65
    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 1.0157 185.241
    1614 no value sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Subtracted 217.446 3.246 214.2
    FOXA2 hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] Divided 217.233 1.0156 213.897
    RAP2B ras-related protein rap-2b. [swissprot;acc:p17964] Low confidence 202.026 1.02085 197.9
    ZNF622 zinc finger-like protein 9. [refseq;acc:nm_033414] Subtracted 202.494 4.088 198.406
    1615 CXXC1 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] Divided 205.179 1.02085 200.988

    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/