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 [...,...].
    Gene Rank Filtered Value Type Network Comparison Type Interaction Map description red green network_comparison
    Results: HTML CSV LaTeX Showing element 501 to 550 of 19268 in total
    Value Type  : Ranked
    Rank
    		Filtered
    		Network Comparison Type
    		Interaction Map
    		description
    		red
    		green
    		network_comparison
    63 1 Divided High confidence guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 266.865 336.178 1.25973
    Low confidence putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] 265.688 239.902 1.10749
    Subtracted High confidence 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] 260.532 204.309 56.223
    Low confidence jun dimerization protein. [refseq;acc:nm_130469] 202.802 182.73 20.072
    64 0 Divided High confidence similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 15264 20387 1.33563
    Low confidence selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 14463 11356 1.2736
    Subtracted High confidence hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 8152.55 11134.8 2982.25
    Low confidence early hematopoietic zinc finger. [refseq;acc:nm_015461] 5850.23 8903.28 3053.05
    1 Divided High confidence guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 266.868 336.159 1.25965
    Low confidence transcription factor jun-d. [swissprot;acc:p17535] 202.709 183.361 1.10552
    Subtracted High confidence 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] 260.532 204.309 56.223
    Low confidence fos-related antigen 2. [swissprot;acc:p15408] 202.793 182.961 19.832
    65 0 Divided High confidence e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] 7853.67 10406.3 1.32502
    Low confidence alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 10172.1 12943.5 1.27245
    Subtracted High confidence oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 8519.83 11453 2933.17
    Low confidence p28 ing5. [refseq;acc:nm_032329] 12418.8 9391.47 3027.33
    1 Divided High confidence guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 267.136 336.077 1.25807
    Low confidence transcription factor jun-b. [swissprot;acc:p17275] 202.728 183.388 1.10546
    Subtracted High confidence 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
    Low confidence protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 202.792 182.974 19.818
    66 0 Divided High confidence heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] 11461 15180 1.32449
    Low confidence kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] 7923.89 10030.4 1.26584
    Subtracted High confidence nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] 9830 6909 2921
    Low confidence blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526] 11290 8270.5 3019.5
    1 Divided High confidence guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 267.136 336.077 1.25807
    Low confidence mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] 221.902 200.783 1.10518
    Subtracted High confidence uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 187.458 243.678 56.22
    Low confidence fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 202.79 183.017 19.773
    67 0 Divided High confidence presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] 10793.5 14291.5 1.32408
    Low confidence dynamin-like 120 kda protein, mitochondrial precursor (optic atrophy 1 gene protein). [swissprot;acc:o60313] 11636.2 14697.6 1.26309
    Subtracted High confidence purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 8932.56 11823.3 2890.74
    Low confidence protein kinase, lysine deficient 3. [refseq;acc:nm_020922] 13320.5 10324.5 2996
    1 Divided High confidence guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] 267.14 336.075 1.25805
    Low confidence retinoblastoma-associated factor 600. [refseq;acc:nm_020765] 165.535 149.799 1.10505
    Subtracted High confidence 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] 187.458 243.677 56.219
    Low confidence putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] 195.817 215.516 19.699
    68 0 Divided High confidence purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 8932.56 11823.3 1.32362
    Low confidence repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] 7803.58 9824.6 1.25899
    Subtracted High confidence 40s ribosomal protein s26. [swissprot;acc:p02383] 14269.7 17098 2828.3
    Low confidence fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 9449.27 12378.5 2929.23
    1 Divided High confidence guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] 267.139 336.075 1.25805
    Low confidence 60s ribosomal protein l37a. [swissprot;acc:p12751] 239.692 217.005 1.10455
    Subtracted High confidence 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] 187.462 243.673 56.211
    Low confidence potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 225.735 245.308 19.573
    69 0 Divided High confidence collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] 7704.7 10174.1 1.32051
    Low confidence transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] 15870.7 12610.3 1.25855
    Subtracted High confidence elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] 16290.7 13464.8 2825.9
    Low confidence nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] 9830 6909 2921
    1 Divided High confidence guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] 267.14 336.075 1.25805
    Low confidence testis-specific protein tex28. [swissprot;acc:o15482] 259.517 235.017 1.10425

    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
    - 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/