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 Value Type description Filtered Interaction Map Network Comparison Type green network_comparison red
    Results: HTML CSV LaTeX Showing element 1 to 50 of 8289 in total
    Value Type  : Ranked
    Filtered  : 1
    Network Comparison Type  : Divided
    Rank
    		description
    		Interaction Map
    		green
    		network_comparison
    		red
    1 carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Low confidence 32 2 16
    putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] High confidence 24 2.4 10
    2 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Low confidence 330 1.47982 223
    mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] High confidence 28 1.86667 15
    3 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Low confidence 330 1.47982 223
    cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] High confidence 28 1.86667 15
    4 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Low confidence 330 1.47982 223
    cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] High confidence 28 1.86667 15
    5 cytohesin 4. [swissprot;acc:q9uia0]
    lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 330 1.47982 223
    6 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] High confidence 28 1.86667 15
    oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Low confidence 240 1.325 318
    7 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] High confidence 322 1.49767 215
    oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence 240 1.325 318
    8 hbs1-like. [refseq;acc:nm_006620] High confidence 322 1.49767 215
    oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] Low confidence 240 1.325 318
    9 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 44 1.31818 58
    xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] High confidence 309 1.45755 212
    10 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Low confidence 44 1.31818 58
    protein x 0004. [refseq;acc:nm_016301] High confidence 309 1.45755 212
    11 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Low confidence 28.4944 1.30966 37.318
    rad50-interacting protein 1. [refseq;acc:nm_021930] High confidence 232 1.45259 337
    12 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]
    vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Low confidence 28.5242 1.30933 37.3475
    13 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 29.1831 1.30207 37.9984
    protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] High confidence 212.554 1.3585 288.754
    14 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 75.3531 1.32952 56.6768
    vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Low confidence 29.1831 1.30207 37.9984
    15 microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] High confidence 75.3948 1.32914 56.7244
    protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Low confidence 202.362 1.26035 255.046
    16 microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] High confidence 75.3954 1.32913 56.7252
    thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Low confidence 247.246 1.2355 305.472
    17 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] High confidence 75.447 1.32866 56.7841
    gbp protein isoform a. [refseq;acc:nm_017870] Low confidence 247.213 1.23537 305.399
    18 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] High confidence 245.247 1.32082 185.678
    jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Low confidence 247.169 1.2352 305.303
    19 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] High confidence 245.247 1.32082 185.678
    trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] Low confidence 246.824 1.23387 304.548
    20 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] High confidence 245.247 1.32082 185.678
    trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] Low confidence 246.737 1.23354 304.359
    21 myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] High confidence 245.247 1.32082 185.678
    phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] Low confidence 163 1.21472 198
    22 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] High confidence 245.247 1.32082 185.678
    n33 protein. [swissprot;acc:q13454] Low confidence 163 1.21472 198
    23 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] High confidence 44 1.31818 58
    implantation-associated protein. [refseq;acc:nm_032121] Low confidence 163 1.21472 198
    24 histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773] 228.509 1.21355 188.298
    pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] High confidence 44 1.31818 58
    25 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] Low confidence 238.476 1.20094 286.396
    pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] High confidence 44 1.31818 58

    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/