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 Value Type Network Comparison Type Interaction Map Filtered red green 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
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    1 carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] CPD Low confidence 16 32 2
    putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] UBAC1 High confidence 10 24 2.4
    2 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] LAMP1 Low confidence 223 330 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] no value High confidence 15 28 1.86667
    3 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] CDK4 Low confidence 223 330 1.47982
    cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] PSCD1 High confidence 15 28 1.86667
    4 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] CDK6 Low confidence 223 330 1.47982
    cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] PSCD2 High confidence 15 28 1.86667
    5 cytohesin 4. [swissprot;acc:q9uia0] PSCD4
    lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] LAMP2 Low confidence 223 330 1.47982
    6 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] PSCD3 High confidence 15 28 1.86667
    oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] OSBPL6 Low confidence 318 240 1.325
    7 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] HLX High confidence 215 322 1.49767
    oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] OSBPL3 Low confidence 318 240 1.325
    8 hbs1-like. [refseq;acc:nm_006620] HBS1L High confidence 215 322 1.49767
    oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] OSBPL7 Low confidence 318 240 1.325
    9 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] MRPS17 58 44 1.31818
    xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] XAB1 High confidence 212 309 1.45755
    10 mitochondrial solute carrier protein. [refseq;acc:nm_145305] SLC25A43 Low confidence 58 44 1.31818
    protein x 0004. [refseq;acc:nm_016301] ATPBD1C High confidence 212 309 1.45755
    11 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] BEST1 Low confidence 37.318 28.4944 1.30966
    rad50-interacting protein 1. [refseq;acc:nm_021930] RINT1 High confidence 337 232 1.45259
    12 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] RHOBTB2
    vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] BEST4 Low confidence 37.3475 28.5242 1.30933
    13 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] no value 37.9984 29.1831 1.30207
    protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] UFC1 High confidence 288.754 212.554 1.3585
    14 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] ATG4A 56.6768 75.3531 1.32952
    vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] BEST2 Low confidence 37.9984 29.1831 1.30207
    15 microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] MAP1LC3B High confidence 56.7244 75.3948 1.32914
    protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] UFC1 Low confidence 255.046 202.362 1.26035
    16 microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] MAP1LC3A High confidence 56.7252 75.3954 1.32913
    thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] JMJD1C Low confidence 305.472 247.246 1.2355
    17 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] ATG4B High confidence 56.7841 75.447 1.32866
    gbp protein isoform a. [refseq;acc:nm_017870] TMEM132A Low confidence 305.399 247.213 1.23537
    18 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] GBE1 High confidence 185.678 245.247 1.32082
    jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] JMJD1A Low confidence 305.303 247.169 1.2352
    19 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] PYGB High confidence 185.678 245.247 1.32082
    trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] PRSS3 Low confidence 304.548 246.824 1.23387
    20 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] PYGL High confidence 185.678 245.247 1.32082
    trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] PRSS1 Low confidence 304.359 246.737 1.23354
    21 myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] MYO15A High confidence 185.678 245.247 1.32082
    phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] PIGF Low confidence 198 163 1.21472
    22 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] PYGM High confidence 185.678 245.247 1.32082
    n33 protein. [swissprot;acc:q13454] TUSC3 Low confidence 198 163 1.21472
    23 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] MRPS17 High confidence 58 44 1.31818
    implantation-associated protein. [refseq;acc:nm_032121] no value Low confidence 198 163 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] HINT1 188.298 228.509 1.21355
    pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] PANK1 High confidence 58 44 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] CYP27B1 Low confidence 286.396 238.476 1.20094
    pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] PANK2 High confidence 58 44 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
    - 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/