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 Network Comparison Type Hugo description Value Type Interaction Map Filtered network_comparison red green
    Results: HTML CSV LaTeX Showing element 1 to 50 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		description
    		network_comparison
    		red
    		green
    1 Divided UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 2.4 10 24
    Subtracted HLX homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 107 215 322
    2 Divided 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] 1.86667 15 28
    Subtracted HBS1L hbs1-like. [refseq;acc:nm_006620] 107 215 322
    3 Divided PSCD1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 1.86667 15 28
    Subtracted RINT1 rad50-interacting protein 1. [refseq;acc:nm_021930] 105 337 232
    4 Divided PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 1.86667 15 28
    Subtracted RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 105 337 232
    5 Divided PSCD4 cytohesin 4. [swissprot;acc:q9uia0] 1.86667 15 28
    Subtracted XAB1 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 97 212 309
    6 Divided PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 1.86667 15 28
    Subtracted ATPBD1C protein x 0004. [refseq;acc:nm_016301] 97 212 309
    7 Divided HLX homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 1.49767 215 322
    Subtracted UFC1 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 76.2 288.754 212.554
    8 Divided HBS1L hbs1-like. [refseq;acc:nm_006620] 1.49767 215 322
    Subtracted JPH3 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 74 288 362
    9 Divided XAB1 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 1.45755 212 309
    Subtracted JPH2 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 74 288 362
    10 Divided ATPBD1C protein x 0004. [refseq;acc:nm_016301] 1.45755 212 309
    Subtracted SMPD2 sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] 74 288 362
    11 Divided RINT1 rad50-interacting protein 1. [refseq;acc:nm_021930] 1.45259 337 232
    Subtracted TMEM33 db83 protein. [swissprot;acc:p57088] 74 288 362
    12 Divided RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1.45259 337 232
    Subtracted no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 69.377 266.856 336.233
    13 Divided UFC1 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 1.3585 288.754 212.554
    Subtracted GNG12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] 69.377 266.856 336.233
    14 Divided ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 1.32952 56.6768 75.3531
    Subtracted GNG4 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 69.328 266.863 336.191
    15 Divided MAP1LC3B microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 1.32914 56.7244 75.3948
    Subtracted GNG3 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 69.327 266.863 336.19
    16 Divided MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 1.32913 56.7252 75.3954
    Subtracted GNG8 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 69.32 266.864 336.184
    17 Divided ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 1.32866 56.7841 75.447
    Subtracted GNG5 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 69.318 266.864 336.182
    18 Divided GBE1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 1.32082 185.678 245.247
    Subtracted GNG10 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 69.316 266.865 336.181
    19 Divided PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 1.32082 185.678 245.247
    Subtracted no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 69.313 266.865 336.178
    20 Divided PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 1.32082 185.678 245.247
    Subtracted GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 69.291 266.868 336.159
    21 Divided MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 1.32082 185.678 245.247
    Subtracted TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] 69.094 325.586 256.492
    22 Divided PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 1.32082 185.678 245.247
    Subtracted PPP1R14A protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 69 322 253
    23 Divided MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 1.31818 58 44
    Subtracted MFAP4 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 69 322 253
    24 Divided PANK1 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 1.31818 58 44
    Subtracted PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] 69 322 253
    25 Divided PANK2 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 1.31818 58 44
    Subtracted FCN2 ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 69 322 253

    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/