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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 201 to 250 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    51 KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Rooted 27.7254 44.0299 1.58807
    NEUROD4 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Measured 779.167 1390.33 1.78438
    SPATA6 spermatogenesis associated 6. [refseq;acc:nm_019073] Ranked 133 105 1.26667
    STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Squared 28994.2 17134.8 1.69212
    52 AMPD2 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Ranked 133 105 1.26667
    CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Measured 779.167 1390.33 1.78438
    NEURL neuralized-like. [refseq;acc:nm_004210] Rooted 27.9107 44.1656 1.58239
    VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Squared 28994.2 17134.8 1.69212
    53 CDK2AP1 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Measured 779.167 1390.33 1.78438
    CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] Squared 28994.2 17134.8 1.69212
    JUNB transcription factor jun-b. [swissprot;acc:p17275] Ranked 201.144 158.868 1.26611
    NDUFS4 nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Rooted 30.8986 46.4619 1.50369
    54 DTX2 deltex 2. [refseq;acc:nm_020892] Measured 1618.84 2651.88 1.63814
    JUND transcription factor jun-d. [swissprot;acc:p17535] Ranked 200.941 158.941 1.26425
    MAGED4 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Squared 219048 129762 1.68808
    UFC1 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Rooted 40.0958 58.7986 1.46645
    55 DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Measured 1629.21 2662.12 1.63399
    KCND2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Rooted 41.6734 28.9323 1.44038
    MAGEE2 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Squared 219048 129762 1.68808
    PRKRAP1 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Ranked 320.927 254.434 1.26134
    56 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 266.856 336.233 1.25998
    melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Squared 219048 129762 1.68808
    CTH cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Rooted 41.6851 28.9509 1.43986
    PBK t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Measured 1631.67 2664.55 1.63302
    57 GNG12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Ranked 266.856 336.233 1.25998
    KCND3 potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Rooted 41.6879 28.9554 1.43973
    KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Measured 1631.67 2664.55 1.63302
    MAGEA11 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Squared 219048 129762 1.68808
    58 GNG4 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Ranked 266.863 336.191 1.25979
    KCND1 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Rooted 41.6969 28.9696 1.43933
    KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Measured 1631.67 2664.55 1.63302
    MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Squared 219048 129762 1.68808
    59 no value hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
    GNG3 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Ranked 266.863 336.19 1.25978
    KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Measured 1631.67 2664.55 1.63302
    NDUFA12 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Rooted 37.2205 52.2064 1.40262
    60 GBE1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Measured 4489.19 2765.82 1.6231
    GNG8 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Ranked 266.864 336.184 1.25976
    MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Squared 219048 129762 1.68808
    SON son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Rooted 35.6294 49.8119 1.39806
    61 GNG5 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Ranked 266.864 336.182 1.25975
    KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Rooted 43.4291 31.7159 1.36932
    NDN necdin. [swissprot;acc:q99608] Squared 219048 129762 1.68808
    PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Measured 4489.19 2765.82 1.6231
    62 GNG10 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Ranked 266.865 336.181 1.25974
    KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Rooted 43.4519 31.7522 1.36847
    MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Squared 219048 129762 1.68808
    PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Measured 4489.19 2765.82 1.6231
    63 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Ranked 266.865 336.178 1.25973
    KCNIP2 kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] Rooted 43.4554 31.7576 1.36835

    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/