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 Hugo Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 56474 to 56523 of 66312 in total
    Network Comparison Type  : Subtracted
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    2915 Squared neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [swissprot;acc:p32076] HPCA Low confidence 1556.4 45387.3 43830.9
    Rooted high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13] HMG4L 2.3311 70.9179 73.249
    mitochondrial solute carrier protein. [refseq;acc:nm_016612] SLC25A37 High confidence 0 0 0
    2916 Measured ribose-phosphate pyrophosphokinase i (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase i) (ppribp) (prs-i). [swissprot;acc:p09329] PRPS1L1
    tera protein. [refseq;acc:nm_021238] FAM60A Low confidence 226.68 7807.44 8034.12
    Ranked ribose-phosphate pyrophosphokinase i (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase i) (ppribp) (prs-i). [swissprot;acc:p09329] PRPS1L1 High confidence 0 0 0
    ribosomal protein s6 kinase (ec 2.7.1.-) (s6k) (p70-s6k). [swissprot;acc:p23443] RPS6KB1 Low confidence 3.362 200.341 196.979
    Squared ribose-phosphate pyrophosphokinase i (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase i) (ppribp) (prs-i). [swissprot;acc:p09329] PRPS1L1 High confidence 0 0 0
    ubiquitin associated protein 2 isoform 1; ad-012 protein. [refseq;acc:nm_018449] UBAP2 Low confidence 1556.1 43709.5 42153.4
    Rooted ribose-phosphate pyrophosphokinase i (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase i) (ppribp) (prs-i). [swissprot;acc:p09329] PRPS1L1 High confidence 0 0 0
    steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] ESRRA Low confidence 2.3307 72.8776 75.2083
    2917 Measured myotubularin related protein 6 (ec 3.1.3.-). [swissprot;acc:q9y217] MTMR6 226.63 8036.46 8263.09
    t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227] CCT6A High confidence 0 0 0
    Ranked myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] no value Low confidence 3.361 200.05 196.689
    t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227] CCT6A High confidence 0 0 0
    Squared
    visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [swissprot;acc:p37235] HPCAL1 Low confidence 1555.9 45386 43830.1
    Rooted t-cell acute lymphocytic leukemia-1 protein (tal-1 protein) (stem cell protein) (t-cell leukemia/lymphoma-5 protein). [swissprot;acc:p17542] TAL1 2.3304 71.2144 73.5448
    t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227] CCT6A High confidence 0 0 0
    2918 Measured myotubularin related protein 8. [refseq;acc:nm_017677] MTMR8 Low confidence 226.63 8036.46 8263.09
    nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] GBAS High confidence 0 0 0
    Ranked myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] no value Low confidence 3.36 200.04 196.68
    nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] GBAS High confidence 0 0 0
    Squared hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] no value Low confidence 1555.3 45741.3 44186
    nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] GBAS High confidence 0 0 0
    Rooted lyl-1 protein (lymphoblastic leukemia derived sequence 1). [swissprot;acc:p12980] LYL1 Low confidence 2.3304 71.2143 73.5447
    nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] GBAS High confidence 0 0 0
    2919 Measured glycine receptor alpha-1 chain precursor (glycine receptor 48 kda subunit) (strychnine binding subunit). [swissprot;acc:p23415] GLRA1
    upstream regulatory element binding protein 1; hect domain protein lasu1; bj-hcc-24 tumor antigen. [refseq;acc:nm_031407] HUWE1 Low confidence 226.63 8036.46 8263.09
    Ranked gamma-tubulin complex component 2 (gcp-2) (spindle pole body protein spc97 homolog) (hspc97) (hgcp2) (h103p). [swissprot;acc:q9bsj2] TUBGCP2 3.36 200.725 197.365
    glycine receptor alpha-1 chain precursor (glycine receptor 48 kda subunit) (strychnine binding subunit). [swissprot;acc:p23415] GLRA1 High confidence 0 0 0
    Squared
    heat shock 70 kda protein 4 (heat shock 70-related protein apg-2) (hsp70ry). [swissprot;acc:p34932] HSPA4 Low confidence 1555.2 44586.3 43031.1
    Rooted cug triplet repeat rna-binding protein 1 (cug-bp1) (rna-binding protein brunol-2) (deadenylation factor cug-bp) (50 kda nuclear polyadenylated rna-binding protein) (eden-bp). [swissprot;acc:q92879] CUGBP1 2.3298 71.3474 73.6772
    glycine receptor alpha-1 chain precursor (glycine receptor 48 kda subunit) (strychnine binding subunit). [swissprot;acc:p23415] GLRA1 High confidence 0 0 0
    2920 Measured glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] GLRA3
    myotubularin related protein 7 (ec 3.1.3.-) (fragment). [swissprot;acc:q9y216] MTMR7 Low confidence 226.63 8036.46 8263.09
    Ranked glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] GLRA3 High confidence 0 0 0
    splicing factor u2af 35 kda subunit (u2 auxiliary factor 35 kda subunit) (u2 snrnp auxiliary factor small subunit). [swissprot;acc:q01081] U2AF1 Low confidence 3.359 202.057 198.698
    Squared glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] GLRA3 High confidence 0 0 0
    rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565] ARHGDIA Low confidence 1554.1 43124.4 41570.3
    Rooted glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] GLRA3 High confidence 0 0 0
    rna-binding protein with multiple splicing (rbp-ms). [swissprot;acc:q93062] RBPMS Low confidence 2.3297 71.3834 73.7131
    2921 Measured ell-associated factor 2; uncharacterized bone marrow protein bm040; testosterone regulated apoptosis inducer and tumor suppressor. [refseq;acc:nm_018456] EAF2 High confidence 0 0 0
    presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] no value Low confidence 226.62 7914.19 8140.81
    Ranked ell-associated factor 2; uncharacterized bone marrow protein bm040; testosterone regulated apoptosis inducer and tumor suppressor. [refseq;acc:nm_018456] EAF2 High confidence 0 0 0
    guanidinoacetate n-methyltransferase (ec 2.1.1.2). [swissprot;acc:q14353] GAMT Low confidence 3.359 199.28 195.921
    Squared ell-associated factor 2; uncharacterized bone marrow protein bm040; testosterone regulated apoptosis inducer and tumor suppressor. [refseq;acc:nm_018456] EAF2 High confidence 0 0 0
    protein farnesyltransferase alpha subunit (ec 2.5.1.-) (caax farnesyltransferase alpha subunit) (ras proteins prenyltransferase alpha) (ftase-alpha). [swissprot;acc:p49354] FNTA Low confidence 1553.7 45034.9 43481.2
    Rooted ell-associated factor 2; uncharacterized bone marrow protein bm040; testosterone regulated apoptosis inducer and tumor suppressor. [refseq;acc:nm_018456] EAF2 High confidence 0 0 0

    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/