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 Interaction Map Hugo network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 30 to 79 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Interaction Map
    		Hugo
    		network_comparison
    		red
    		green
    4 Squared lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence LAMP2 19.4914 1362.75 69.9153
    Rooted hbs1-like. [refseq;acc:nm_006620] High confidence HBS1L 1.92839 50.9657 26.4292
    lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence LAMP2 2.10117 48.9847 23.3131
    5 Measured junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] High confidence JPH3 3.39764 1153.5 339.5
    oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Low confidence OSBPL6 2.86965 736.5 2113.5
    Ranked cytohesin 4. [swissprot;acc:q9uia0] High confidence PSCD4 1.86667 15 28
    lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence LAMP2 1.47982 223 330
    Squared junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] High confidence JPH3 11.544 314.926 27.2805
    oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Low confidence OSBPL6 8.23493 128.386 1057.25
    Rooted junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] High confidence JPH3 1.84327 33.9632 18.4255
    oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Low confidence OSBPL6 1.69401 27.1385 45.9728
    6 Measured junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] High confidence JPH2 3.39764 1153.5 339.5
    oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence OSBPL3 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] High confidence PSCD3 1.86667 15 28
    oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Low confidence OSBPL6 1.325 318 240
    Squared junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] High confidence JPH2 11.544 314.926 27.2805
    oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence OSBPL3 8.23493 128.386 1057.25
    Rooted junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] High confidence JPH2 1.84327 33.9632 18.4255
    oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence OSBPL3 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] High confidence SMPD2 3.39764 1153.5 339.5
    Ranked homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] HLX 1.49767 215 322
    oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence OSBPL3 1.325 318 240
    Squared oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] OSBPL7 8.23493 128.386 1057.25
    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] High confidence SMPD2 11.544 314.926 27.2805
    Rooted oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] Low confidence OSBPL7 1.69401 27.1385 45.9728
    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] High confidence SMPD2 1.84327 33.9632 18.4255
    8 Measured db83 protein. [swissprot;acc:p57088] TMEM33 3.39764 1153.5 339.5
    phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] Low confidence PIGF 1.54317 3278 5058.5
    Ranked hbs1-like. [refseq;acc:nm_006620] High confidence HBS1L 1.49767 215 322
    oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] Low confidence OSBPL7 1.325 318 240
    Squared db83 protein. [swissprot;acc:p57088] High confidence TMEM33 11.544 314.926 27.2805
    phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] Low confidence PIGF 2.38136 2543.26 6056.43
    Rooted db83 protein. [swissprot;acc:p57088] High confidence TMEM33 1.84327 33.9632 18.4255
    thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Low confidence JMJD1C 1.49674 31.8641 47.6922
    9 Measured n33 protein. [swissprot;acc:q13454] TUSC3 1.54317 3278 5058.5
    tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] High confidence TOB2 3.21581 398.5 1281.5
    Ranked 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Low confidence MRPS17 1.31818 58 44
    xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] High confidence XAB1 1.45755 212 309
    Squared n33 protein. [swissprot;acc:q13454] Low confidence TUSC3 2.38136 2543.26 6056.43
    tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] High confidence TOB2 10.3414 37.5863 388.696
    Rooted gbp protein isoform a. [refseq;acc:nm_017870] Low confidence TMEM132A 1.49599 31.8923 47.7107
    tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] High confidence TOB2 1.79326 19.9625 35.798
    10 Measured implantation-associated protein. [refseq;acc:nm_032121] Low confidence no value 1.54317 3278 5058.5
    tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] High confidence TOB1 3.21581 398.5 1281.5
    Ranked mitochondrial solute carrier protein. [refseq;acc:nm_145305] Low confidence SLC25A43 1.31818 58 44
    protein x 0004. [refseq;acc:nm_016301] High confidence ATPBD1C 1.45755 212 309
    Squared implantation-associated protein. [refseq;acc:nm_032121] Low confidence no value 2.38136 2543.26 6056.43
    tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] High confidence TOB1 10.3414 37.5863 388.696
    Rooted jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Low confidence JMJD1A 1.49501 31.9296 47.7352

    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/