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 [...,...].
    Network Comparison Type Rank Gene Value Type description Hugo Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 80 to 129 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    10 Rooted tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] TOB1 High confidence 1.79326 19.9625 35.798
    11 Measured dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] DAB2IP 3.21581 398.5 1281.5
    thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] JMJD1C Low confidence 1.53861 1917.64 2950.5
    Ranked bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] BEST1 1.30966 37.318 28.4944
    rad50-interacting protein 1. [refseq;acc:nm_021930] RINT1 High confidence 1.45259 337 232
    Squared 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] MRPS17 Low confidence 1.80879 106226 192141
    dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] DAB2IP High confidence 10.3414 37.5863 388.696
    Rooted 1.79326 19.9625 35.798
    trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] PRSS3 Low confidence 1.48738 32.2231 47.928
    12 Measured cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] CPEB4 High confidence 3.21581 398.5 1281.5
    gbp protein isoform a. [refseq;acc:nm_017870] TMEM132A Low confidence 1.5371 1921.96 2954.24
    Ranked rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] RHOBTB2 High confidence 1.45259 337 232
    vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] BEST4 Low confidence 1.30933 37.3475 28.5242
    Squared cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] CPEB4 High confidence 10.3414 37.5863 388.696
    mitochondrial solute carrier protein. [refseq;acc:nm_145305] SLC25A43 Low confidence 1.80879 106226 192141
    Rooted cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] CPEB4 High confidence 1.79326 19.9625 35.798
    trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] PRSS1 Low confidence 1.48549 32.2966 47.9763
    13 Measured cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] CPEB3 High confidence 3.21581 398.5 1281.5
    jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] JMJD1A Low confidence 1.5351 1927.68 2959.19
    Ranked nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] no value 1.30207 37.9984 29.1831
    protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] UFC1 High confidence 1.3585 288.754 212.554
    Squared carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] CPD Low confidence 1.63062 395912 242799
    cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] CPEB3 High confidence 10.3414 37.5863 388.696
    Rooted 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] CYP27B1 Low confidence 1.33896 39.2301 52.5277
    cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] CPEB3 High confidence 1.79326 19.9625 35.798
    14 Measured ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] RASAL2 3.21581 398.5 1281.5
    trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] PRSS3 Low confidence 1.51983 1972.65 2998.1
    Ranked cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] ATG4A High confidence 1.32952 56.6768 75.3531
    vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] BEST2 Low confidence 1.30207 37.9984 29.1831
    Squared atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] no value 1.56161 7744.68 4959.41
    ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] RASAL2 High confidence 10.3414 37.5863 388.696
    Rooted cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] CYP27A1 Low confidence 1.33864 39.2489 52.5401
    ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] RASAL2 High confidence 1.79326 19.9625 35.798
    15 Measured trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] PRSS1 Low confidence 1.51612 1983.91 3007.85
    xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] XAB1 High confidence 3.06659 2671 871
    Ranked microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] MAP1LC3B 1.32914 56.7244 75.3948
    protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] UFC1 Low confidence 1.26035 255.046 202.362
    Squared sperm associated antigen 7. [refseq;acc:nm_004890] SPAG7 1.53438 209554 136572
    xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] XAB1 High confidence 9.40399 1688.58 179.56
    Rooted cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973] CYP24A1 Low confidence 1.32836 39.8493 52.9343
    gbp protein isoform a. [refseq;acc:nm_017870] TMEM132A High confidence 1.77158 23.9771 42.4773
    16 Measured 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] MRPS17 Low confidence 1.34491 21185 28492
    protein x 0004. [refseq;acc:nm_016301] ATPBD1C High confidence 3.06659 2671 871
    Ranked microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] MAP1LC3A 1.32913 56.7252 75.3954
    thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] JMJD1C Low confidence 1.2355 305.472 247.246
    Squared bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] BEST1 1.42441 333556 475119
    protein x 0004. [refseq;acc:nm_016301] ATPBD1C High confidence 9.40399 1688.58 179.56
    Rooted tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] TOB2 Low confidence 1.27952 38.4152 49.1529
    xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] XAB1 High confidence 1.75117 51.6817 29.5127
    17 Measured dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] DGCR14 2.96739 460 1365

    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/