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 description Gene Hugo Network Comparison Type Value Type red Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 932 to 981 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    233 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] MYH13 Measured 9035 7279.6 1.24114
    234 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] CHRAC1 Ranked 287.41 256.835 1.11905
    melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] no value Rooted 137.446 120.823 1.13758
    neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] CHRNA6 Squared 42411.6 55802.1 1.31573
    ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] RPS6KC1 Measured 5181.2 6410.58 1.23728
    235 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] MAGEA9 Rooted 137.446 120.823 1.13758
    nitrogen fixation cluster-like. [refseq;acc:nm_014301] ISCU Squared 42411.6 55802.1 1.31573
    phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] PAH Ranked 227.357 254.15 1.11785
    ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] no value Measured 5181.2 6410.58 1.23728
    236 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] MAGEA8 Rooted 137.446 120.823 1.13758
    pp3111 protein. [refseq;acc:nm_022156] DUS1L Ranked 227.357 254.15 1.11785
    spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] TXNL4A Measured 4723.53 5828.46 1.23392
    star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] STARD13 Squared 42411.6 55802.1 1.31573
    237 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] MAGEC1 Rooted 137.446 120.823 1.13758
    star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] STARD8 Squared 42411.6 55802.1 1.31573
    syntaxin 18. [swissprot;acc:q9p2w9] STX18 Ranked 227.357 254.15 1.11785
    u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] LSM5 Measured 4567.04 5631.2 1.23301
    238 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] MAGEA4 Rooted 137.446 120.823 1.13758
    neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] CHRNA2 Squared 42411.6 55802.1 1.31573
    protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] PPP1R7 Measured 27642.5 22440.4 1.23182
    rd protein. [swissprot;acc:p18615] no value Ranked 227.357 254.15 1.11785
    239 carboxypeptidase b precursor. [refseq;acc:nm_020361] CPA6 Measured 7711.38 6265.8 1.23071
    glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] GSTO1 Ranked 227.357 254.15 1.11785
    melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] no value Rooted 137.446 120.823 1.13758
    mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] MAPKAPK3 Squared 42411.6 55802.1 1.31573
    240 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] AIG1 Ranked 227.357 254.15 1.11785
    mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] CPA3 Measured 7711.36 6265.79 1.23071
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] MAGEA10 Rooted 137.446 120.823 1.13758
    mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] MAPK14 Squared 42411.6 55802.1 1.31573
    241 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] ATP5F1 Ranked 227.357 254.15 1.11785
    melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 Rooted 137.446 120.823 1.13758
    neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] CHRNA4 Squared 42411.6 55802.1 1.31573
    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 Measured 7711.31 6265.76 1.23071
    242 j domain containing protein 1. [swissprot;acc:q9ukb3] DNAJC12 Ranked 227.357 254.15 1.11785
    max protein. [swissprot;acc:p25912] MAX Measured 4640.26 5704.87 1.22943
    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] MAGED2 Rooted 137.446 120.823 1.13758
    neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] CHRNA3 Squared 42411.6 55802.1 1.31573
    243 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] HOMER2 Measured 4246.95 5208.98 1.22652
    sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] SNX13 Ranked 227.357 254.15 1.11785
    sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] SPHK2 Squared 42411.6 55802.1 1.31573
    trophinin. [swissprot;acc:q12816] TRO Rooted 137.446 120.823 1.13758
    244 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] GSTO2 Ranked 227.357 254.15 1.11785
    dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] NCBP2L Squared 14728.8 19330.8 1.31245
    myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] MYO5B Rooted 146.94 167.046 1.13683
    ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] COQ7 Measured 4250.14 5211.25 1.22614
    245 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] GBE1 Squared 8875.01 6768.05 1.31131
    homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] HOMER1 Measured 4251.65 5212.33 1.22595
    myosin vc (myosin 5c). [swissprot;acc:q9nqx4] MYO5C Rooted 146.94 167.046 1.13683
    small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] SNRPD3 Ranked 226.109 202.333 1.11751
    246 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] EIF4G3 237.312 212.363 1.11748

    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/