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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 6408 to 6457 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Value Type
    		Network Comparison Type
    		red
    		green
    		network_comparison
    801 werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Squared Subtracted 20613.1 24595.9 3982.8
    802 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Measured 779.167 1390.33 611.163
    cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Squared 19987.6 23960.7 3973.1
    pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Divided 20131.3 23416.5 1.16319
    synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] Ranked Subtracted 212.386 221.785 9.399
    target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Measured Divided 6455.66 7168.82 1.11047
    testis-specific protein tex28. [swissprot;acc:o15482] Ranked 212.386 221.785 1.04425
    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 51.3516 1.06474
    translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Subtracted 82.1841 86.2754 4.0913
    803 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 Divided 22573.3 26254.5 1.16308
    calsyntenin-1 precursor. [swissprot;acc:o94985] Rooted Subtracted 82.1841 86.2754 4.0913
    doc-1 related protein (doc-1r). [swissprot;acc:o75956] Measured 779.167 1390.33 611.163
    importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Divided 6455.02 7167.96 1.11045
    similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] Ranked 212.386 221.785 1.04425
    syntaxin 1b. [swissprot;acc:q15531] Subtracted 9.399
    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 Divided 54.6759 51.3516 1.06474
    transforming protein rhoc (h9). [swissprot;acc:p08134] Squared Subtracted 19987.6 23960.7 3973.1
    804 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 Divided 74.3877 79.1931 1.0646
    a kindred of iglon. [refseq;acc:nm_173808] Ranked 212.386 221.785 1.04425
    melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084] Subtracted 9.399
    nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Measured Divided 6770.78 7517.97 1.11036
    neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Subtracted 779.167 1390.33 611.163
    succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Rooted 82.1841 86.2754 4.0913
    thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Squared 19987.6 23960.7 3973.1
    transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Divided 24954.5 29022.6 1.16302
    805 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 79.1513 1.0645
    3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] Squared Subtracted 19987.6 23960.7 3973.1
    60s ribosomal protein l39. [swissprot;acc:p02404] Measured Divided 4708.61 5226.71 1.11003
    ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] Ranked 212.386 221.785 1.04425
    dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Squared 15384.8 17890 1.16284
    dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] Ranked Subtracted 212.386 221.785 9.399
    neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Measured 779.167 1390.33 611.163
    protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Rooted 82.184 86.2753 4.0913
    806 40s ribosomal protein s26. [swissprot;acc:p02383] Divided 62.4161 58.6426 1.06435
    60s ribosomal protein l18a. [swissprot;acc:q02543] Measured 4708.61 5226.71 1.11003
    inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] Ranked 212.386 221.785 1.04425
    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 29715.4 1.16278
    maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] Ranked Subtracted 267.447 276.773 9.326
    neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Measured 779.167 1390.33 611.163
    thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Rooted 82.184 86.2753 4.0913
    transforming protein rhoa (h12). [swissprot;acc:p06749] Squared 19987.6 23960.7 3973.1
    807 40s ribosomal protein s19. [swissprot;acc:p39019] Measured Divided 4708.61 5226.71 1.11003
    chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Subtracted 779.167 1390.33 611.163
    gk001 protein. [refseq;acc:nm_020198] Rooted 82.184 86.2753 4.0913
    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] Squared Divided 25560.1 29720.6 1.16277
    mad protein (max dimerizer). [swissprot;acc:q05195] Subtracted 17248.4 21214 3965.6
    mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Rooted Divided 62.416 58.6426 1.06435
    palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] Ranked 212.386 221.785 1.04425
    trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102] Subtracted 218.521 227.796 9.275
    808 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 223.186 213.912 9.274

    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
    - 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/