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 description Network Comparison Type Filtered Interaction Map red green network_comparison
    Results: HTML CSV LaTeX Showing element 501 to 550 of 14920 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Rank
    		Value Type
    		description
    		Filtered
    		red
    		green
    		network_comparison
    63 Squared melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 1 219048 129762 1.68808
    protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 0 1.24091 0.365145 3.3984
    Rooted dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 18.1049 12.6095 1.43581
    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] 1 43.4554 31.7576 1.36835
    64 Measured glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 4489.19 2765.82 1.6231
    phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] 0 0.00001 18 1800000
    Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 1 266.868 336.159 1.25965
    similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 0 15264 20387 1.33563
    Squared melanoma antigen, family b, 6. [refseq;acc:nm_173523] 1 219048 129762 1.68808
    tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 0 50.8715 15.2519 3.33542
    Rooted 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 1 63.8686 47.2654 1.35128
    muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 0 15.7225 22.5496 1.43422
    65 Measured neuralized-like. [refseq;acc:nm_004210] 1 1657.68 2690.25 1.6229
    rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] 0 18 0.00001 1800000
    Ranked 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
    guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 1 267.136 336.077 1.25807
    Squared 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 0 50.642 15.1833 3.33538
    melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 1 219048 129762 1.68808
    Rooted 60s ribosomal protein l21. [swissprot;acc:p46778] 0 20.5734 29.2291 1.42072
    glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 1 63.8686 47.2654 1.35128
    66 Measured 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] 1991.03 3221.38 1.61795
    soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] 0 688.436 385.626 1.78524
    Ranked guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 1 267.136 336.077 1.25807
    heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] 0 11461 15180 1.32449
    Squared dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 1797.76 558.241 3.2204
    melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 1 219048 129762 1.68808
    Rooted glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 63.8686 47.2654 1.35128
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 0 30.9855 21.9983 1.40854
    67 Measured beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 1 6475.5 10307.5 1.59177
    filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 0 1603 898 1.78508
    Ranked guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] 1 267.14 336.075 1.25805
    presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] 0 10793.5 14291.5 1.32408
    Squared filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 608.191 190.865 3.1865
    melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 1 219048 129762 1.68808
    Rooted isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 0 11.0051 15.3166 1.39177
    myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 1 63.8686 47.2654 1.35128
    68 Measured beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 6475.5 10307.5 1.59177
    protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] 0 198.964 351.772 1.76802
    Ranked guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] 1 267.139 336.075 1.25805
    purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 0 8932.56 11823.3 1.32362
    Squared melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 1 219048 129762 1.68808
    mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 31.36 0.00001 3136000
    Rooted alpha crystallin a chain. [swissprot;acc:p02489] 6.22183 8.63381 1.38766
    glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 1 63.8686 47.2654 1.35128
    69 Measured dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 0 1593 2804 1.7602
    spermatogenesis associated 6. [refseq;acc:nm_019073] 1 6475.5 10307.5 1.59177
    Ranked collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] 0 7704.7 10174.1 1.32051
    guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] 1 267.14 336.075 1.25805
    Squared melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 219048 129762 1.68808
    protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] 0 16.2406 50.7408 3.12432

    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/