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 [...,...].
    Gene description Rank Hugo Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 182 to 231 of 473 in total
    Value Type  : Ranked
    Network Comparison Type  : Subtracted
    Interaction Map  : High confidence
    red  : 0
    Filtered  : 1
    green  : 0
    network_comparison  : 0
    description
    		Rank
    		Hugo
    integrin beta-2 precursor (cell surface adhesion glycoproteins lfa- 1/cr3/p150,95 beta-subunit) (cd18) (complement receptor c3 beta- subunit). [swissprot;acc:p05107] 2873 ITGB2
    integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106] 3195 ITGB3
    integrin beta-7 precursor. [swissprot;acc:p26010] 2951 ITGB7
    interleukin enhancer binding factor 2; nuclear factor of activated t-cells, 45-kda. [refseq;acc:nm_004515] 2930 ILF2
    jerky protein homolog like (hhmjg). [swissprot;acc:q9y4a0] 2775 JRKL
    kiaa1194. [refseq;acc:nm_015455] 3061 CNOT6
    lactamase, beta 2. [refseq;acc:nm_016027] 2914 LACTB2
    langerhans cell specific c-type lectin. [refseq;acc:nm_015717] 3046 CD207
    late endosomal/lysosomal mp1 interacting protein (p14) (hspc003). [swissprot;acc:q9y2q5] 3044 no value
    leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] 3017 LRRFIP1
    leucine rich repeat (in flii) interacting protein 2. [refseq;acc:nm_006309] 3153 LRRFIP2
    likely ortholog of mouse c-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 13; c-type lectin 13; likely ortholog of rat kupffer cell c-type lectin receptor. [refseq;acc:nm_173535] 2898 CLEC4F
    lyl-1 protein (lymphoblastic leukemia derived sequence 1). [swissprot;acc:p12980] 3107 LYL1
    lysosomal trafficking regulator (beige homolog). [swissprot;acc:q99698] 2929 LYST
    mab-21-like protein 1; mab-21-like 1. [refseq;acc:nm_005584] 2786 MAB21L1
    mab-21-like protein 2; mab-21-like 2. [refseq;acc:nm_006439] 2783 MAB21L2
    mago nashi protein homolog. [swissprot;acc:p50606] 2864 MAGOH
    major centromere autoantigen b (centromere protein b) (cenp-b). [swissprot;acc:p07199] 3013 CENPB
    malate dehydrogenase, cytoplasmic (ec 1.1.1.37). [swissprot;acc:p40925] 3213 MDH1
    mam domain containing glycosylphosphatidylinositol anchor 1; glycosyl-phosphatidyl-inositol-mam. [refseq;acc:nm_153487] 3070 MDGA1
    membrane-bound transcription factor site 2 protease (ec 3.4.24.-) (site-2 protease) (sterol-regulatory element-binding proteins intramembrane protease). [swissprot;acc:o43462] 3215 MBTPS2
    microfibrillar-associated protein 1. [swissprot;acc:p55081] 2949 MFAP1
    microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650] 2880 no value
    mitochondrial 28s ribosomal protein s30 (s30mt) (mrp-s30) (programmed cell death protein 9) (bm047). [swissprot;acc:q9np92] 3063 MRPS30
    mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932] 2825 no value
    mitochondrial deoxynucleotide carrier (mitochondrial uncoupling protein 1). [swissprot;acc:q9hc21] 3014 SLC25A19
    mitochondrial ribosomal protein s7; 30s ribosomal protein s7 homolog. [refseq;acc:nm_015971] 3016 MRPS7
    mitochondrial solute carrier protein. [refseq;acc:nm_016612] 2915 SLC25A37
    mitogen-activated protein kinase kinase 1 interacting protein 1 (mek binding partner 1) (mp1) (pro2783). [swissprot;acc:q9uha4] 3084 MAP2K1IP1
    mo25 protein (cgi-66). [swissprot;acc:q9y376] 2976 CAB39
    mo25-like protein. [swissprot;acc:q9h9s4] 3116 CAB39L
    mob-lak. [refseq;acc:nm_130807] 2812 MOBKL2A
    mondoa. [refseq;acc:nm_014938] 2800 MLXIP
    mothers against decapentaplegic homolog interacting protein (madh-interacting protein) (smad anchor for receptor activation) (receptor activation anchor) (hsara) (novel serine protease) (nsp). [swissprot;acc:o95405] 2887 ZFYVE9
    muts protein homolog 4. [swissprot;acc:o15457] 3194 MSH4
    muts protein homolog 5. [swissprot;acc:o43196] 3148 no value
    myeloblast kiaa0230 (fragment). [sptrembl;acc:q92626] 3000 PXDN
    myosin heavy chain, nonmuscle type a (cellular myosin heavy chain, type a) (nonmuscle myosin heavy chain-a) (nmmhc-a). [swissprot;acc:p35579] 3140 MYH9
    myosin heavy chain, nonmuscle type b (cellular myosin heavy chain, type b) (nonmuscle myosin heavy chain-b) (nmmhc-b). [swissprot;acc:p35580] 2988 MYH10
    myosin heavy chain, smooth muscle isoform (smmhc). [swissprot;acc:p35749] 2985 MYH11
    myotubularin-related protein 1 (ec 3.1.3.-). [swissprot;acc:q13613] 3190 MTMR1
    myotubularin-related protein 2 (ec 3.1.3.-). [swissprot;acc:q13614] 3166 MTMR2
    n-acetylglucosamine kinase (ec 2.7.1.59) (glcnac kinase). [swissprot;acc:q9uj70] 3022 NAGK
    nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] 3005 NDUFA5
    nadh-ubiquinone oxidoreductase 24 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3). [swissprot;acc:p19404] 2795 NDUFV2
    nadh-ubiquinone oxidoreductase 30 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-30kd) (ci-30kd). [swissprot;acc:o75489] 3081 PTPMT1
    nadh-ubiquinone oxidoreductase 39 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-39kd) (ci-39kd). [swissprot;acc:q16795] 2954 NDUFA9
    nadh-ubiquinone oxidoreductase 49 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-49kd) (ci-49kd). [swissprot;acc:o75306] 2878 NDUFS2
    nanos (fragment). [sptrembl;acc:q8wy41] 2803 no value
    neuromedin u receptor 2. [refseq;acc:nm_020167] 2991 NMUR2

    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/