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 Network Comparison Type Hugo Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 63474 to 63523 of 66312 in total
    Interaction Map  : Low confidence
    Filtered  : 1
    Rank
    		description
    		Network Comparison Type
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    4707 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] Divided SLC25A6 Squared 46240.3 45568 1.01475
    grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] Subtracted GRPEL2 Measured 8594 8707.75 113.75
    guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Divided GNAT1 Rooted 71.2809 72.5571 1.0179
    mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Subtracted CPA3 75.8019 77.1275 1.3256
    melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Divided MAGED2 Ranked 178.882 179.908 1.00574
    syntaxin 6. [swissprot;acc:o43752] Subtracted STX6 203.037 201.937 1.1
    ubiquitin-conjugating enzyme e2 g1 (ec 6.3.2.19) (ubiquitin-protein ligase g1) (ubiquitin carrier protein g1) (e217k) (ubc7). [swissprot;acc:q99462] UBE2G1 Squared 41417.3 40777.8 639.5
    4708 carboxypeptidase b precursor. [refseq;acc:nm_020361] CPA6 Rooted 75.8029 77.1271 1.3242
    cell matrix adhesion regulator (cell adhesion regulatory protein) (cell adhesion regulator). [swissprot;acc:q04762] Divided no value Measured 7369.62 7472.14 1.01391
    dnaj homolog subfamily a member 4. [swissprot;acc:q8ww22] DNAJA4 Squared 48727 49442.6 1.01469
    integrin alpha-5 precursor (fibronectin receptor alpha subunit) (integrin alpha-f) (vla-5) (cd49e). [swissprot;acc:p08648] Subtracted ITGA5 Measured 8713.6 8827.14 113.54
    orm1-like 3. [refseq;acc:nm_139280] ORMDL3 Ranked 201.328 202.427 1.099
    protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Divided PPP1R2 Rooted 78.4056 79.8048 1.01785
    tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Subtracted TOB1 Squared 16570.2 15932.3 637.9
    trophinin. [swissprot;acc:q12816] Divided TRO Ranked 178.882 179.908 1.00574
    4709 asparaginase-like 1 protein. [refseq;acc:nm_025080] ASRGL1 Measured 7450.83 7554.21 1.01387
    cda11 protein. [refseq;acc:nm_032026] TATDN1 Squared 47223.2 46541.8 1.01464
    guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] GNAI2 Rooted 71.256 72.5259 1.01782
    integrin alpha-v precursor (vitronectin receptor alpha subunit) (cd51 antigen). [swissprot;acc:p06756] Subtracted ITGAV Measured 8713.6 8827.14 113.54
    nuclear protein zap3 (zap113). [swissprot;acc:p49750] Divided YLPM1 Ranked 199.992 198.86 1.00569
    ormdl2. [refseq;acc:nm_014182] Subtracted ORMDL2 201.337 202.436 1.099
    oxysterol-binding protein 2 (oxysterol binding protein-related protein 4) (osbp-related protein 4) (orp-4). [swissprot;acc:q969r2] OSBP2 Squared 49688.8 50325.2 636.4
    plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] CPB2 Rooted 75.8045 77.1275 1.323
    4710 adenomatous polyposis coli protein (apc protein). [swissprot;acc:p25054] Divided APC Measured 6233.66 6148.69 1.01382
    galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Subtracted LGALS4 Squared 44487.8 43852.9 634.9
    integrin alpha-8. [swissprot;acc:p53708] ITGA8 Measured 8713.6 8827.14 113.54
    myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, drosophila). [refseq;acc:nm_182931] Divided MLL5 Rooted 71.3636 72.6354 1.01782
    polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] SMOX Squared 51948.6 52708.4 1.01463
    sarcoma amplified sequence. [swissprot;acc:q12999] TSPAN31 Ranked 201.93 200.79 1.00568
    smooth muscle cell associated protein-1. [refseq;acc:nm_017979] Subtracted UNC45A Rooted 71.4045 72.7265 1.322
    tight junction protein zo-1 (zonula occludens 1 protein) (zona occludens 1 protein) (tight junction protein 1). [swissprot;acc:q07157] TJP1 Ranked 203.102 202.006 1.096
    4711 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Divided no value Rooted 69.8173 71.0591 1.01779
    60s ribosomal protein l9. [swissprot;acc:p32969] Measured 7416.2 7518.37 1.01378
    cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Subtracted CPSF4 Rooted 77.6629 78.98 1.3171
    coactosin-like protein. [swissprot;acc:q14019] COTL1 Ranked 203.334 202.239 1.095
    galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Divided LGALS4 Squared 44487.8 43852.9 1.01448
    glioma amplified on chromosome 1 protein precursor. [swissprot;acc:o75325] LRRN2 Ranked 206.04 204.881 1.00566
    integrin alpha-iib precursor (platelet membrane glycoprotein iib) (gpalpha iib) (gpiib) (cd41 antigen). [swissprot;acc:p08514] Subtracted ITGA2B Measured 8713.6 8827.14 113.54
    tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] TOB2 Squared 16434.5 15804.8 629.7
    4712 atp-dependent rna helicase a (nuclear dna helicase ii) (ndh ii) (dead-box protein 9). [swissprot;acc:q08211] DHX9 Rooted 68.3812 69.6927 1.3115
    dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] Divided DDB1 Squared 46361.4 45706 1.01434
    glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] Subtracted CNDP1 47618.7 46989.3 629.4
    guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Divided GNAI1 Rooted 71.2428 72.5093 1.01778
    leucine rich repeat neuronal 1. [refseq;acc:nm_020873] LRRN1 Ranked 206.041 204.886 1.00564
    paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367] Subtracted PAX6 Measured 7480.38 7593.05 112.67
    prkca-binding protein (protein kinase c-alpha binding protein) (protein interacting with c kinase 1). [swissprot;acc:q9nrd5] PICK1 Ranked 201.562 202.655 1.093
    tyrosine 3-monooxygenase (ec 1.14.16.2) (tyrosine 3-hydroxylase) (th). [swissprot;acc:p07101] Divided TH Measured 8490.93 8607.91 1.01378
    4713 60s ribosomal protein l7. [swissprot;acc:p18124] Subtracted no value Rooted 69.6335 70.9401 1.3066
    guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Divided GNAI3 71.2428 72.5093 1.01778
    leucine rich repeat neuronal 3; leucine-rich repeat protein, neuronal 3. [refseq;acc:nm_018334] LRRN3 Ranked 206.041 204.886 1.00564

    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/