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 Filtered Interaction Map Network Comparison Type red network_comparison green
    Results: HTML CSV LaTeX Showing element 3180 to 3229 of 12912 in total
    Filtered  : 1
    Interaction Map  : High confidence
    Network Comparison Type  : Divided
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		network_comparison
    		green
    795 TOP2B dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Measured 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 xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] Squared 25842.1 1.16451 30093.4
    SERPINB6 placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] Ranked 224.244 1.04578 234.511
    SETMAR set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] Rooted 54.765 1.06481 51.4319
    797 no value cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] Ranked 224.244 1.04578 234.511
    KPNB1 importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] Measured 6834.54 1.11061 7590.49
    LSAMP limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Squared 22535.2 1.16433 26238.4
    SSRP1 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] Rooted 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 opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] Squared 22587.2 1.1642 26296.1
    SERPINB1 leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740] Ranked 224.244 1.04578 234.511
    TBL1X transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] Measured 6834.54 1.11061 7590.49
    799 no value neurotrimin precursor (hnt). [swissprot;acc:q9p121] Squared 22623.7 1.16412 26336.8
    FCER2 low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Rooted 54.765 1.06481 51.4319
    SQSTM1 sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] Ranked 221.965 1.04501 212.404
    TBL1Y transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Measured 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 phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] Squared 22210.6 1.1634 25839.9
    SCP2 nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] Ranked 221.965 1.04501 212.404
    SUPT16H chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Rooted 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 beta-catenin (pro2286). [swissprot;acc:p35222] Ranked 224.445 1.04445 214.894
    KPNA3 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] Measured 6456.35 1.1105 7169.75
    PMM1 phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Squared 22208.7 1.16322 25833.6
    802 no value 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] Rooted 54.6759 1.06474 51.3516
    PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Squared 20131.3 1.16319 23416.5
    TEX28P2 testis-specific protein tex28. [swissprot;acc:o15482] Ranked 212.386 1.04425 221.785
    TOE1 target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Measured 6455.66 1.11047 7168.82
    803 C3orf60 similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] Ranked 212.386 1.04425 221.785
    EPRS 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] Squared 22573.3 1.16308 26254.5
    GTF2H1 tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] Rooted 54.6759 1.06474 51.3516
    KPNA4 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Measured 6455.02 1.11045 7167.96
    804 AGPAT2 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] Rooted 74.3877 1.0646 79.1931
    NDUFB9 nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Measured 6770.78 1.11036 7517.97
    NEGR1 a kindred of iglon. [refseq;acc:nm_173808] Ranked 212.386 1.04425 221.785
    TKTL1 transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Squared 24954.5 1.16302 29022.6
    805 no value 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] Rooted 74.3557 1.0645 79.1513
    60s ribosomal protein l39. [swissprot;acc:p02404] Measured 4708.61 1.11003 5226.71
    ANKRA2 ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] Ranked 212.386 1.04425 221.785
    POLE dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Squared 15384.8 1.16284 17890
    806 no value 40s ribosomal protein s26. [swissprot;acc:p02383] Rooted 62.4161 1.06435 58.6426
    60s ribosomal protein l18a. [swissprot;acc:q02543] Measured 4708.61 1.11003 5226.71
    GPR84 inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] Ranked 212.386 1.04425 221.785
    IMPA1 inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218] Squared 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 palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] Ranked 212.386 1.04425 221.785
    RPS19 40s ribosomal protein s19. [swissprot;acc:p39019] Measured 4708.61 1.11003 5226.71
    TIMM22 mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Rooted 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/