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 3208 to 3257 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		red
    		network_comparison
    		green
    1604 CLK2 protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] Divided 214.984 1.01593 211.614
    1605 FOXA1 hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] 217.322 1.01592 213.916
    ZNF207 zinc finger protein 207. [swissprot;acc:o43670] Subtracted 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
    MORF4L2 transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [swissprot;acc:q15014] Subtracted 228.477 3.27 231.747
    1607 no value transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] 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
    1608 GSPT1 g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] Subtracted 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
    UGP2 utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Divided 208.113 1.0158 204.876
    1610 RPUSD2 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Subtracted 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
    TMBIM4 z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Subtracted 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
    TMBIM1 pp1201 protein. [refseq;acc:nm_022152] Subtracted 217.446 3.246 214.2
    1613 FAIM2 lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]
    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 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
    1615 POLE2 dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] 246.38 242.596
    SREBF1 sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] Subtracted 217.446 3.246 214.2
    1616 NAGS n-acetylglutamate synthase. [refseq;acc:nm_153006] Divided 223.179 1.01538 226.611
    TMEM189 ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] Subtracted 208.106 3.239 204.867
    1617 SHMT1 serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] Divided 221.045 1.01537 217.699
    UGP2 utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Subtracted 208.113 3.237 204.876
    1618 TCEA2 transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [swissprot;acc:q15560] Divided 227.768 1.01527 231.246
    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] Subtracted 208.122 3.236 204.886
    1619 no value survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] 228.496 3.233 231.729
    transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] Divided 227.768 1.01527 231.246
    1620 ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] Subtracted 228.496 3.233 231.729
    GTF2B transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] Divided 228.611 1.01521 225.185
    1621 RAC3 ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Subtracted 228.496 3.233 231.729
    ZNHIT3 thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] Divided 228.611 1.01521 225.185
    1622 NHP2L1 nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769]
    NUP54 nucleoporin 54kda; nucleoporin p54. [refseq;acc:nm_017426] Subtracted 228.496 3.233 231.729
    1623 NUFIP1 nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] Divided 228.611 1.01521 225.185
    RAC2 ras-related c3 botulinum toxin substrate 2 (p21-rac2) (small g protein) (gx). [swissprot;acc:p15153] Subtracted 228.496 3.233 231.729
    1624 MCM5 dna replication licensing factor mcm5 (cdc46 homolog) (p1-cdc46). [swissprot;acc:p33992]
    PDCD11 rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] Divided 230.643 1.01518 227.194
    1625 RPUSD2 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] 217.446 1.01515 214.2
    SIP1 survival of motor neuron protein-interacting protein 1 (smn- interacting protein 1) (component of gems 2) (gemin2). [swissprot;acc:o14893] Subtracted 228.496 3.233 231.729
    1626 DDX20 probable atp-dependent rna helicase ddx20 (dead-box protein 20) (dead- box protein dp 103) (component of gems 3) (gemin3). [swissprot;acc:q9uhi6]
    TMBIM4 z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Divided 217.446 1.01515 214.2
    1627 SHMT2 serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897] Subtracted 220.686 3.205 217.481
    TMBIM1 pp1201 protein. [refseq;acc:nm_022152] Divided 217.446 1.01515 214.2
    1628 CTBP1 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] Subtracted 196.215 3.197 193.018
    FAIM2 lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Divided 217.446 1.01515 214.2
    1629 no value sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]

    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/