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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 412 to 461 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Value Type
    		red
    		green
    		network_comparison
    52 HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Subtracted Squared 173408 242989 69581
    MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Rooted 137.446 120.823 16.623
    NEURL neuralized-like. [refseq;acc:nm_004210] Divided 27.9107 44.1656 1.58239
    RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Subtracted Ranked 350 290 60
    VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Divided Squared 28994.2 17134.8 1.69212
    53 no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted 173408 242989 69581
    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] Divided 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
    NDN necdin. [swissprot;acc:q99608] Subtracted Rooted 137.446 120.823 16.623
    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] Divided 30.8986 46.4619 1.50369
    Subtracted Ranked 318.982 259.004 59.978
    PAPOLA poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Measured 23326.5 19296.4 4030.1
    54 DTX2 deltex 2. [refseq;acc:nm_020892] Divided 1618.84 2651.88 1.63814
    EXOC2 exocyst complex component sec5. [swissprot;acc:q96kp1] Subtracted 23316 19288.8 4027.2
    GBE1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Ranked 185.678 245.247 59.569
    HOXD4 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Squared 173408 242989 69581
    JUND transcription factor jun-d. [swissprot;acc:p17535] Divided Ranked 200.941 158.941 1.26425
    MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Subtracted Rooted 137.446 120.823 16.623
    MAGED4 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Divided 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
    HOXB5 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Subtracted Squared 173408 242989 69581
    KCND2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Divided Rooted 41.6734 28.9323 1.44038
    MAGEE2 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Squared 219048 129762 1.68808
    MAGEF1 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Subtracted Rooted 137.446 120.823 16.623
    PAPOLG poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Measured 23303.1 19279.5 4023.6
    PRKRAP1 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Divided Ranked 320.927 254.434 1.26134
    PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Subtracted 185.678 245.247 59.569
    56 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Divided 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
    HOXA5 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Subtracted Squared 173408 242989 69581
    MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] Rooted 137.446 120.823 16.623
    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] Divided Measured 1631.67 2664.55 1.63302
    PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Subtracted Ranked 185.678 245.247 59.569
    RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Measured 20911 24908.5 3997.5
    57 no value homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Squared 173408 242989 69581
    melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Rooted 137.446 120.823 16.623
    GNG12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Divided 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
    MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Subtracted Ranked 185.678 245.247 59.569
    RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Measured 20911 24908.5 3997.5
    58 GNG4 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Divided Ranked 266.863 336.191 1.25979
    HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Subtracted Squared 173408 242989 69581
    KCND1 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Divided 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

    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/