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 [...,...].
    Network Comparison Type Rank Gene Value Type description Hugo Interaction Map Filtered network_comparison red green
    Results: HTML CSV LaTeX Showing element 1 to 50 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    1 Measured lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] LAMP1 Low confidence 4.4149 2399.5 543.5
    rad50-interacting protein 1. [refseq;acc:nm_021930] RINT1 High confidence 5.31521 450.5 2394.5
    Ranked carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] CPD Low confidence 2 16 32
    putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] UBAC1 High confidence 2.4 10 24
    Squared lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] LAMP1 Low confidence 19.4914 1362.75 69.9153
    rad50-interacting protein 1. [refseq;acc:nm_021930] RINT1 High confidence 28.2513 48.0356 1357.07
    Rooted lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] LAMP1 Low confidence 2.10117 48.9847 23.3131
    rad50-interacting protein 1. [refseq;acc:nm_021930] RINT1 High confidence 2.30547 21.225 48.9336
    2 Measured cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] CDK4 Low confidence 4.4149 2399.5 543.5
    rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] RHOBTB2 High confidence 5.31521 450.5 2394.5
    Ranked lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] LAMP1 Low confidence 1.47982 223 330
    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 1.86667 15 28
    Squared cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] CDK4 Low confidence 19.4914 1362.75 69.9153
    rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] RHOBTB2 High confidence 28.2513 48.0356 1357.07
    Rooted cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] CDK4 Low confidence 2.10117 48.9847 23.3131
    rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] RHOBTB2 High confidence 2.30547 21.225 48.9336
    3 Measured cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] CDK6 Low confidence 4.4149 2399.5 543.5
    homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] HLX High confidence 3.71868 2597.5 698.5
    Ranked cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] CDK4 Low confidence 1.47982 223 330
    cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] PSCD1 High confidence 1.86667 15 28
    Squared cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] CDK6 Low confidence 19.4914 1362.75 69.9153
    homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] HLX High confidence 13.8285 1596.92 115.48
    Rooted cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] CDK6 Low confidence 2.10117 48.9847 23.3131
    homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] HLX High confidence 1.92839 50.9657 26.4292
    4 Measured hbs1-like. [refseq;acc:nm_006620] HBS1L 3.71868 2597.5 698.5
    lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] LAMP2 Low confidence 4.4149 2399.5 543.5
    Ranked cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] CDK6 1.47982 223 330
    cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] PSCD2 High confidence 1.86667 15 28
    Squared hbs1-like. [refseq;acc:nm_006620] HBS1L 13.8285 1596.92 115.48
    lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] LAMP2 Low confidence 19.4914 1362.75 69.9153
    Rooted hbs1-like. [refseq;acc:nm_006620] HBS1L High confidence 1.92839 50.9657 26.4292
    lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] LAMP2 Low confidence 2.10117 48.9847 23.3131
    5 Measured junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] JPH3 High confidence 3.39764 1153.5 339.5
    oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] OSBPL6 Low confidence 2.86965 736.5 2113.5
    Ranked cytohesin 4. [swissprot;acc:q9uia0] PSCD4 High confidence 1.86667 15 28
    lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] LAMP2 Low confidence 1.47982 223 330
    Squared junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] JPH3 High confidence 11.544 314.926 27.2805
    oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] OSBPL6 Low confidence 8.23493 128.386 1057.25
    Rooted junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] JPH3 High confidence 1.84327 33.9632 18.4255
    oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] OSBPL6 Low confidence 1.69401 27.1385 45.9728
    6 Measured junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] JPH2 High confidence 3.39764 1153.5 339.5
    oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] OSBPL3 Low confidence 2.86965 736.5 2113.5
    Ranked cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] PSCD3 High confidence 1.86667 15 28
    oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] OSBPL6 Low confidence 1.325 318 240
    Squared junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] JPH2 High confidence 11.544 314.926 27.2805
    oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] OSBPL3 Low confidence 8.23493 128.386 1057.25
    Rooted junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] JPH2 High confidence 1.84327 33.9632 18.4255
    oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] OSBPL3 Low confidence 1.69401 27.1385 45.9728
    7 Measured oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] OSBPL7 2.86965 736.5 2113.5
    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 High confidence 3.39764 1153.5 339.5

    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/