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

    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/