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 Value Type Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 230 to 279 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    Hugo
    description
    Network Comparison Type
    Interaction Map
    red
    green
    network_comparison
    58 GNG4 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Divided High confidence 266.863 336.191 1.25979
    PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Subtracted 185.678 245.247 59.569
    UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Low confidence 155.56 133.876 21.684
    59 GNG3 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Divided High confidence 266.863 336.19 1.25978
    KCND2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Subtracted 269.278 327.709 58.431
    MTUS1 mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] Low confidence 221.902 200.783 21.119
    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] Divided 233.134 210.267 1.10875
    60 CTH cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Subtracted High confidence 269.254 327.655 58.401
    FOSL2 fos-related antigen 2. [swissprot;acc:p15408] Divided Low confidence 202.793 182.961 1.10839
    GNG8 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] High confidence 266.864 336.184 1.25976
    LENG4 malignant cell expression-enhanced gene/tumor progression-enhanc. [refseq;acc:nm_024298] Subtracted Low confidence 211 231.635 20.635
    61 APBA1 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] 229.144 208.803 20.341
    FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Divided 202.792 182.974 1.10831
    GNG5 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] High confidence 266.864 336.182 1.25975
    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] Subtracted 269.248 327.642 58.394
    62 FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Low confidence 202.802 182.73 20.072
    FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Divided 202.79 183.017 1.10804
    GNG10 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] High confidence 266.865 336.181 1.25974
    KCND1 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Subtracted 269.23 327.601 58.371
    63 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Divided 266.865 336.178 1.25973
    jun dimerization protein. [refseq;acc:nm_130469] Subtracted Low confidence 202.802 182.73 20.072
    NFYC nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] High confidence 260.532 204.309 56.223
    RBM7 putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Divided Low confidence 265.688 239.902 1.10749
    64 FOSL2 fos-related antigen 2. [swissprot;acc:p15408] Subtracted 202.793 182.961 19.832
    GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Divided High confidence 266.868 336.159 1.25965
    JUND transcription factor jun-d. [swissprot;acc:p17535] Low confidence 202.709 183.361 1.10552
    NFYA ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Subtracted High confidence 260.532 204.309 56.223
    65 no value serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] 187.457 243.678 56.221
    FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Low confidence 202.792 182.974 19.818
    GNAQ guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Divided High confidence 267.136 336.077 1.25807
    JUNB transcription factor jun-b. [swissprot;acc:p17275] Low confidence 202.728 183.388 1.10546
    66 FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Subtracted 202.79 183.017 19.773
    GNA11 guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Divided High confidence 267.136 336.077 1.25807
    MTUS1 mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] Low confidence 221.902 200.783 1.10518
    PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Subtracted High confidence 187.458 243.678 56.22
    67 AHCYL1 putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Low confidence 195.817 215.516 19.699
    GNAT2 guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Divided High confidence 267.14 336.075 1.25805
    PPP2R2B serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Subtracted 187.458 243.677 56.219
    UBR4 retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Divided Low confidence 165.535 149.799 1.10505
    68 no value 60s ribosomal protein l37a. [swissprot;acc:p12751] 239.692 217.005 1.10455
    GNAZ guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] High confidence 267.139 336.075 1.25805
    KCND2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Subtracted Low confidence 225.735 245.308 19.573
    PPP2R2C serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] High confidence 187.462 243.673 56.211
    69 no value putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Low confidence 195.851 215.424 19.573
    GNAT1 guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Divided High confidence 267.14 336.075 1.25805
    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] Subtracted 284.753 228.934 55.819
    TEX28P2 testis-specific protein tex28. [swissprot;acc:o15482] Divided Low confidence 259.517 235.017 1.10425
    70 GNAI2 guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] High confidence 267.142 336.074 1.25804
    GOSR2 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] Low confidence 259.517 235.017 1.10425
    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] Subtracted 225.545 244.933 19.388

    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/