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 Value Type Hugo description Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 51 to 100 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		Hugo
    		description
    		Interaction Map
    		network_comparison
    		red
    		green
    7 Ranked HLX homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] High confidence 1.49767 215 322
    OSBPL3 oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence 1.325 318 240
    Squared OSBPL7 oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 8.23493 128.386 1057.25
    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] High confidence 11.544 314.926 27.2805
    Rooted OSBPL7 oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] Low confidence 1.69401 27.1385 45.9728
    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] High confidence 1.84327 33.9632 18.4255
    8 Measured PIGF phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] Low confidence 1.54317 3278 5058.5
    TMEM33 db83 protein. [swissprot;acc:p57088] High confidence 3.39764 1153.5 339.5
    Ranked HBS1L hbs1-like. [refseq;acc:nm_006620] 1.49767 215 322
    OSBPL7 oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] Low confidence 1.325 318 240
    Squared PIGF phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] 2.38136 2543.26 6056.43
    TMEM33 db83 protein. [swissprot;acc:p57088] High confidence 11.544 314.926 27.2805
    Rooted JMJD1C thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Low confidence 1.49674 31.8641 47.6922
    TMEM33 db83 protein. [swissprot;acc:p57088] High confidence 1.84327 33.9632 18.4255
    9 Measured TOB2 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 3.21581 398.5 1281.5
    TUSC3 n33 protein. [swissprot;acc:q13454] Low confidence 1.54317 3278 5058.5
    Ranked MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 1.31818 58 44
    XAB1 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] High confidence 1.45755 212 309
    Squared TOB2 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 10.3414 37.5863 388.696
    TUSC3 n33 protein. [swissprot;acc:q13454] Low confidence 2.38136 2543.26 6056.43
    Rooted TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] 1.49599 31.8923 47.7107
    TOB2 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] High confidence 1.79326 19.9625 35.798
    10 Measured no value implantation-associated protein. [refseq;acc:nm_032121] Low confidence 1.54317 3278 5058.5
    TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] High confidence 3.21581 398.5 1281.5
    Ranked ATPBD1C protein x 0004. [refseq;acc:nm_016301] 1.45755 212 309
    SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Low confidence 1.31818 58 44
    Squared no value implantation-associated protein. [refseq;acc:nm_032121] 2.38136 2543.26 6056.43
    TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] High confidence 10.3414 37.5863 388.696
    Rooted JMJD1A jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Low confidence 1.49501 31.9296 47.7352
    TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] High confidence 1.79326 19.9625 35.798
    11 Measured DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 3.21581 398.5 1281.5
    JMJD1C thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Low confidence 1.53861 1917.64 2950.5
    Ranked BEST1 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] 1.30966 37.318 28.4944
    RINT1 rad50-interacting protein 1. [refseq;acc:nm_021930] High confidence 1.45259 337 232
    Squared DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 10.3414 37.5863 388.696
    MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Low confidence 1.80879 106226 192141
    Rooted DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] High confidence 1.79326 19.9625 35.798
    PRSS3 trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] Low confidence 1.48738 32.2231 47.928
    12 Measured CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] High confidence 3.21581 398.5 1281.5
    TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] Low confidence 1.5371 1921.96 2954.24
    Ranked BEST4 vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] 1.30933 37.3475 28.5242
    RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] High confidence 1.45259 337 232
    Squared CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 10.3414 37.5863 388.696
    SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Low confidence 1.80879 106226 192141
    Rooted CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] High confidence 1.79326 19.9625 35.798
    PRSS1 trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] Low confidence 1.48549 32.2966 47.9763
    13 Measured CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] High confidence 3.21581 398.5 1281.5
    JMJD1A jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Low confidence 1.5351 1927.68 2959.19
    Ranked no value nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 1.30207 37.9984 29.1831
    UFC1 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] High confidence 1.3585 288.754 212.554

    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/