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