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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1 to 50 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		network_comparison
    		green
    1 CPD carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Low confidence 16 2 32
    UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] High confidence 10 2.4 24
    2 no value 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] 15 1.86667 28
    LAMP1 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Low confidence 223 1.47982 330
    3 CDK4 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]
    PSCD1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] High confidence 15 1.86667 28
    4 CDK6 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Low confidence 223 1.47982 330
    PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] High confidence 15 1.86667 28
    5 LAMP2 lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 223 1.47982 330
    PSCD4 cytohesin 4. [swissprot;acc:q9uia0] High confidence 15 1.86667 28
    6 OSBPL6 oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Low confidence 318 1.325 240
    PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] High confidence 15 1.86667 28
    7 HLX homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 215 1.49767 322
    OSBPL3 oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence 318 1.325 240
    8 HBS1L hbs1-like. [refseq;acc:nm_006620] High confidence 215 1.49767 322
    OSBPL7 oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] Low confidence 318 1.325 240
    9 MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 58 1.31818 44
    XAB1 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] High confidence 212 1.45755 309
    10 ATPBD1C protein x 0004. [refseq;acc:nm_016301]
    SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Low confidence 58 1.31818 44
    11 BEST1 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] 37.318 1.30966 28.4944
    RINT1 rad50-interacting protein 1. [refseq;acc:nm_021930] High confidence 337 1.45259 232
    12 BEST4 vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Low confidence 37.3475 1.30933 28.5242
    RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] High confidence 337 1.45259 232
    13 no value nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence 37.9984 1.30207 29.1831
    UFC1 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] High confidence 288.754 1.3585 212.554
    14 ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 56.6768 1.32952 75.3531
    BEST2 vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Low confidence 37.9984 1.30207 29.1831
    15 MAP1LC3B microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] High confidence 56.7244 1.32914 75.3948
    UFC1 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Low confidence 255.046 1.26035 202.362
    16 JMJD1C thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] 305.472 1.2355 247.246
    MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] High confidence 56.7252 1.32913 75.3954
    17 ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 56.7841 1.32866 75.447
    TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] Low confidence 305.399 1.23537 247.213
    18 GBE1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] High confidence 185.678 1.32082 245.247
    JMJD1A jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Low confidence 305.303 1.2352 247.169
    19 PRSS3 trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] 304.548 1.23387 246.824
    PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] High confidence 185.678 1.32082 245.247
    20 PRSS1 trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] Low confidence 304.359 1.23354 246.737
    PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] High confidence 185.678 1.32082 245.247
    21 MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]
    PIGF phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] Low confidence 198 1.21472 163
    22 PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] High confidence 185.678 1.32082 245.247
    TUSC3 n33 protein. [swissprot;acc:q13454] Low confidence 198 1.21472 163
    23 no value implantation-associated protein. [refseq;acc:nm_032121]
    MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] High confidence 58 1.31818 44
    24 HINT1 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] Low confidence 188.298 1.21355 228.509
    PANK1 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] High confidence 58 1.31818 44
    25 CYP27B1 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 286.396 1.20094 238.476
    PANK2 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] High confidence 58 1.31818 44

    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/