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 Value Type description Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 3180 to 3229 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		network_comparison
    		green
    795 TOP2B Measured dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] 6441.14 1.11069 7154.13
    796 no value nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 6834.54 1.11061 7590.49
    REXO4 Squared xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] 25842.1 1.16451 30093.4
    SERPINB6 Ranked placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] 224.244 1.04578 234.511
    SETMAR Rooted set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] 54.765 1.06481 51.4319
    797 no value Ranked cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] 224.244 1.04578 234.511
    KPNB1 Measured importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] 6834.54 1.11061 7590.49
    LSAMP Squared limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] 22535.2 1.16433 26238.4
    SSRP1 Rooted structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] 54.1622 1.06481 57.6725
    798 CLEC4M cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] 54.765 51.4319
    OPCML Squared opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] 22587.2 1.1642 26296.1
    SERPINB1 Ranked leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740] 224.244 1.04578 234.511
    TBL1X Measured transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] 6834.54 1.11061 7590.49
    799 no value Squared neurotrimin precursor (hnt). [swissprot;acc:q9p121] 22623.7 1.16412 26336.8
    FCER2 Rooted low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] 54.765 1.06481 51.4319
    SQSTM1 Ranked sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] 221.965 1.04501 212.404
    TBL1Y Measured transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 6834.54 1.11061 7590.49
    800 NR6A1 orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] 6075.55 1.1105 6746.92
    PMM2 Squared phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] 22210.6 1.1634 25839.9
    SCP2 Ranked nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] 221.965 1.04501 212.404
    SUPT16H Rooted chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] 54.1622 1.06481 57.6725
    801 CD209 cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] 54.765 51.4319
    CTNNB1 Ranked beta-catenin (pro2286). [swissprot;acc:p35222] 224.445 1.04445 214.894
    KPNA3 Measured importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 6456.35 1.1105 7169.75
    PMM1 Squared phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] 22208.7 1.16322 25833.6
    802 no value Rooted tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] 54.6759 1.06474 51.3516
    PRPF31 Squared pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 20131.3 1.16319 23416.5
    TEX28P2 Ranked testis-specific protein tex28. [swissprot;acc:o15482] 212.386 1.04425 221.785
    TOE1 Measured target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] 6455.66 1.11047 7168.82
    803 C3orf60 Ranked similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] 212.386 1.04425 221.785
    EPRS Squared bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] 22573.3 1.16308 26254.5
    GTF2H1 Rooted tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] 54.6759 1.06474 51.3516
    KPNA4 Measured importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] 6455.02 1.11045 7167.96
    804 AGPAT2 Rooted 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] 74.3877 1.0646 79.1931
    NDUFB9 Measured nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] 6770.78 1.11036 7517.97
    NEGR1 Ranked a kindred of iglon. [refseq;acc:nm_173808] 212.386 1.04425 221.785
    TKTL1 Squared transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] 24954.5 1.16302 29022.6
    805 no value Measured 60s ribosomal protein l39. [swissprot;acc:p02404] 4708.61 1.11003 5226.71
    Rooted 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] 74.3557 1.0645 79.1513
    ANKRA2 Ranked ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] 212.386 1.04425 221.785
    POLE Squared dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] 15384.8 1.16284 17890
    806 no value Measured 60s ribosomal protein l18a. [swissprot;acc:q02543] 4708.61 1.11003 5226.71
    Rooted 40s ribosomal protein s26. [swissprot;acc:p02383] 62.4161 1.06435 58.6426
    GPR84 Ranked inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] 212.386 1.04425 221.785
    IMPA1 Squared inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218] 25555.4 1.16278 29715.4
    807 IMPA2 inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [swissprot;acc:o14732] 25560.1 1.16277 29720.6
    PPT1 Ranked palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] 212.386 1.04425 221.785
    RPS19 Measured 40s ribosomal protein s19. [swissprot;acc:p39019] 4708.61 1.11003 5226.71
    TIMM22 Rooted mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] 62.416 1.06435 58.6426
    808 ATPAF2 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]

    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/