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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 894 to 943 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    224 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] MAGEE2 Rooted 137.446 120.823 1.13758
    oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] SLC15A2 Ranked 185.969 165.623 1.12285
    small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] SNRPD1 Squared 14943.9 19771.9 1.32307
    225 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] no value Rooted 137.446 120.823 1.13758
    metaxin 1. [swissprot;acc:q13505] MTX1 Squared 60401.6 79875.7 1.32241
    myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] no value Measured 9035 7279.6 1.24114
    small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] SNRPD2 Ranked 226.471 201.769 1.12243
    226 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] COMP 239.991 269.238 1.12187
    melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] MAGEA11 Rooted 137.446 120.823 1.13758
    myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] MYH4 Measured 9035 7279.6 1.24114
    oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] SLC15A2 Squared 73510.2 55607.3 1.32195
    227 melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] MAGEA2B Rooted 137.446 120.823 1.13758
    myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] MYH8 Measured 9035 7279.6 1.24114
    oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] SLC15A1 Squared 73995.1 56003.7 1.32125
    thrombospondin 3 precursor. [swissprot;acc:p49746] THBS3 Ranked 239.99 269.234 1.12186
    228 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] ECHS1 Squared 57913.5 76336.3 1.31811
    hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] no value Rooted 137.446 120.823 1.13758
    myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] MYH2 Measured 9035 7279.6 1.24114
    sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] SH2D3C Ranked 226.411 202.088 1.12036
    229 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] BCAR3 226.401 202.094 1.12028
    melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] MAGEA6 Rooted 137.446 120.823 1.13758
    mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] MAPK11 Squared 42411.6 55802.1 1.31573
    myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] MYH3 Measured 9035 7279.6 1.24114
    230 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] CSRP1 Ranked 239.35 267.915 1.11934
    myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] MYH1 Measured 9035 7279.6 1.24114
    necdin. [swissprot;acc:q99608] NDN Rooted 137.446 120.823 1.13758
    sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] SPHK1 Squared 42411.6 55802.1 1.31573
    231 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] SHCBP1 Ranked 239.336 267.881 1.11927
    melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] MAGED1 Rooted 137.446 120.823 1.13758
    myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] no value Measured 9035 7279.6 1.24114
    udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] DPAGT1 Squared 42411.6 55802.1 1.31573
    232 dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] MYH7B Measured 9035 7279.6 1.24114
    melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] MAGEF1 Rooted 137.446 120.823 1.13758
    rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] DLC1 Squared 42411.6 55802.1 1.31573
    smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] CSRP2 Ranked 239.336 267.879 1.11926
    233 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] CSRP3 239.32 267.842 1.11918
    map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] MAPKAPK2 Squared 42411.6 55802.1 1.31573
    melanoma antigen, family b, 6. [refseq;acc:nm_173523] MAGEB6B Rooted 137.446 120.823 1.13758
    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

    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/