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 Hugo Network Comparison Type Value Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 6408 to 6457 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		Value Type
    		red
    		green
    		network_comparison
    801 werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] WRNIP1 Subtracted Squared 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] CHD3 Measured 779.167 1390.33 611.163
    cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] CBS Squared 19987.6 23960.7 3973.1
    pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] PRPF31 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] SNAP29 Subtracted Ranked 212.386 221.785 9.399
    target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] TOE1 Divided Measured 6455.66 7168.82 1.11047
    testis-specific protein tex28. [swissprot;acc:o15482] TEX28P2 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] no value 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] SSR4 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] EPRS Divided Squared 22573.3 26254.5 1.16308
    calsyntenin-1 precursor. [swissprot;acc:o94985] CLSTN1 Subtracted Rooted 82.1841 86.2754 4.0913
    doc-1 related protein (doc-1r). [swissprot;acc:o75956] CDK2AP2 Measured 779.167 1390.33 611.163
    importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] KPNA4 Divided 6455.02 7167.96 1.11045
    similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] C3orf60 Ranked 212.386 221.785 1.04425
    syntaxin 1b. [swissprot;acc:q15531] STX1B 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] GTF2H1 Divided Rooted 54.6759 51.3516 1.06474
    transforming protein rhoc (h9). [swissprot;acc:p08134] RHOC Subtracted Squared 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] AGPAT2 Divided Rooted 74.3877 79.1931 1.0646
    a kindred of iglon. [refseq;acc:nm_173808] NEGR1 Ranked 212.386 221.785 1.04425
    melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084] MRPL28 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] NDUFB9 Divided Measured 6770.78 7517.97 1.11036
    neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] NEUROD6 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] no value Rooted 82.1841 86.2754 4.0913
    thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] TST 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] TKTL1 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] no value Rooted 74.3557 79.1513 1.0645
    3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] MPST Subtracted Squared 19987.6 23960.7 3973.1
    60s ribosomal protein l39. [swissprot;acc:p02404] no value Divided Measured 4708.61 5226.71 1.11003
    ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] ANKRA2 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] POLE 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] RFXANK Subtracted Ranked 212.386 221.785 9.399
    neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] NEUROD1 Measured 779.167 1390.33 611.163
    protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] PTPRB Rooted 82.184 86.2753 4.0913
    806 40s ribosomal protein s26. [swissprot;acc:p02383] no value 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] GPR84 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] IMPA1 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] GSTZ1 Subtracted Ranked 267.447 276.773 9.326
    neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] NEUROD4 Measured 779.167 1390.33 611.163
    thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] PRSS16 Rooted 82.184 86.2753 4.0913
    transforming protein rhoa (h12). [swissprot;acc:p06749] RHOA Squared 19987.6 23960.7 3973.1
    807 40s ribosomal protein s19. [swissprot;acc:p39019] RPS19 Divided Measured 4708.61 5226.71 1.11003
    chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] CHD5 Subtracted 779.167 1390.33 611.163
    gk001 protein. [refseq;acc:nm_020198] CCDC47 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] IMPA2 Divided Squared 25560.1 29720.6 1.16277
    mad protein (max dimerizer). [swissprot;acc:q05195] MXD1 Subtracted 17248.4 21214 3965.6
    mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] TIMM22 Divided Rooted 62.416 58.6426 1.06435
    palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] PPT1 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] GART 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] HTATIP 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
    - 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/