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 Network Comparison Type Value Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 59424 to 59473 of 66312 in total
    Interaction Map  : Low confidence
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		Value Type
    		description
    		red
    		green
    		network_comparison
    4200 ZNF256 Subtracted Rooted zinc finger protein 256 (bone marrow zinc finger 3) (bmzf-3). [swissprot;acc:q9y2p7] 76.1821 78.0464 1.8643
    4201 ANAPC1 Measured anaphase-promoting complex 1 (meiotic checkpoint regulator). [refseq;acc:nm_022662] 7735.78 7908.43 172.65
    CAMK1 Divided calcium/calmodulin-dependent protein kinase type i (ec 2.7.1.123) (cam kinase i). [swissprot;acc:q14012] 8292.8 8460.99 1.02028
    CLCN4 Subtracted Ranked chloride channel protein 4 (clc-4). [swissprot;acc:p51793] 203.637 201.584 2.053
    CLCN5 Divided chloride channel protein 5 (clc-5). [swissprot;acc:p51795] 203.636 201.582 1.01019
    COQ6 Squared ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9] 45659.5 44509.3 1.02584
    PTRH2 Subtracted protein cgi-147. [swissprot;acc:q9y3e5] 45848.7 44731.7 1117
    RALBP1 Divided Rooted rala binding protein 1; rala-binding protein. [refseq;acc:nm_006788] 70.388 72.1472 1.02499
    ZNF214 Subtracted zinc finger protein 214 (bwscr2 associated zinc-finger protein 1) (baz 1). [swissprot;acc:q9ul59] 76.1821 78.0464 1.8643
    4202 C12orf10 Divided Squared myg1 protein. [swissprot;acc:q9hb07] 46079.8 44920.2 1.02581
    CS Subtracted citrate synthase, mitochondrial precursor (ec 2.3.3.1). [swissprot;acc:o75390] 45390 44273.2 1116.8
    CYR61 Measured cyr61 protein precursor (cysteine-rich, angiogenic inducer, 61) (insulin-like growth factor-binding protein 10) (gig1 protein). [swissprot;acc:o00622] 7664.06 7836.67 172.61
    FOXJ1 Divided Ranked forkhead box protein j1 (forkhead-related protein fkhl13) (hepatocyte nuclear factor 3 forkhead homolog 4) (hfh-4). [swissprot;acc:q92949] 207.68 205.585 1.01019
    MEIS3 Rooted homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687] 71.8582 73.6528 1.02497
    PRKACG Subtracted Ranked camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 198.254 196.202 2.052
    UBE2B Divided Measured ubiquitin-conjugating enzyme e2 b (ec 6.3.2.19) (ubiquitin-protein ligase b) (ubiquitin carrier protein b) (hr6b) (hhr6b) (e2-17 kda). [swissprot;acc:p23567] 8272.52 8440.2 1.02027
    ZNF7 Subtracted Rooted zinc finger protein 7 (zinc finger protein kox4) (zinc finger protein hf.16). [swissprot;acc:p17097] 76.1821 78.0464 1.8643
    4203 ANKRA2 Divided Ranked ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] 203.592 201.541 1.01018
    Subtracted 2.051
    C9 Divided Measured complement component c9 precursor. [swissprot;acc:p02748] 7699.23 7855.31 1.02027
    MED22 Rooted surfeit locus protein 5. [swissprot;acc:q15528] 71.6608 73.4495 1.02496
    PPA2 Subtracted Measured inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869] 8388.79 8561.39 172.6
    RPL37 Squared 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] 44114.5 42999.9 1114.6
    USP12 Divided ubiquitin carboxyl-terminal hydrolase 12 (ec 3.1.2.15) (ubiquitin thiolesterase 12) (ubiquitin-specific processing protease 12) (deubiquitinating enzyme 12) (ubiquitin hydrolyzing enzyme 1). [swissprot;acc:o75317] 46111.8 44952.9 1.02578
    ZNF41 Subtracted Rooted zinc finger protein 41. [swissprot;acc:p51814] 76.1821 78.0464 1.8643
    4204 C8B Divided Measured complement component c8 beta chain precursor. [swissprot;acc:p07358] 7699.29 7855.39 1.02027
    CLCN3 Subtracted Ranked chloride channel protein 3 (clc-3). [swissprot;acc:p51790] 203.646 201.595 2.051
    CLCN4 Divided chloride channel protein 4 (clc-4). [swissprot;acc:p51793] 203.637 201.584 1.01018
    KMO Subtracted Squared kynurenine 3-monooxygenase (kynurenine 3-hydroxylase). [refseq;acc:nm_003679] 45981.4 44866.8 1114.6
    MAGI2 Divided Rooted atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301] 70.3902 72.1447 1.02493
    SNX5 Subtracted Measured sorting nexin 5. [swissprot;acc:q9y5x3] 7877.71 8050.17 172.46
    ZBTB20 Divided Squared zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [swissprot;acc:q9hc78] 43030.7 41949.8 1.02577
    ZNF630 Subtracted Rooted dj54b20.2 (novel krab box containing c2h2 type zinc finger protein) (fragment). [sptrembl;acc:q96qh9] 76.1821 78.0464 1.8643
    4205 APEX2 Divided Squared apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] 45559.1 44414.9 1.02576
    ATP5L Subtracted Measured atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [swissprot;acc:o75964] 8025.04 8197.43 172.39
    CAMK1D Divided camki-like protein kinase beta isoform. [refseq;acc:nm_153498] 8293.55 8461.5 1.02025
    CLCN3 Ranked chloride channel protein 3 (clc-3). [swissprot;acc:p51790] 203.646 201.595 1.01017
    MAGI1 Rooted bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] 70.4831 72.2402 1.02493
    TGS1 Subtracted Ranked prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] 206.056 204.009 2.047
    TLOC1 Squared translocation protein 1; dtrp1 protein; membrane protein sec62, s.cerevisiae, homolog of. [refseq;acc:nm_003262] 43911.4 42797.5 1113.9
    ZNF157 Rooted zinc finger protein 157 (hzf22). [swissprot;acc:p51786] 76.1821 78.0464 1.8643
    4206 KCND3 Divided Measured 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] 6043.53 5923.6 1.02025
    LYST Rooted lysosomal trafficking regulator (beige homolog). [swissprot;acc:q99698] 72.7962 74.6102 1.02492
    MYC Ranked myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] 203.698 201.652 1.01015
    Subtracted 2.046
    NCK1 Squared cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] 46064.5 44951.2 1113.3
    RAB13 Divided ras-related protein rab-13. [swissprot;acc:p51153] 45777.4 44630 1.02571
    WISP1 Subtracted Measured wnt1 inducible signaling pathway protein 1 isoform 1 precursor; wnt-1 signaling pathway protein 1; wnt1 signaling pathway protein 1; wnt-1 inducible signaling pathway protein 1. [refseq;acc:nm_003882] 7664.94 7837.32 172.38
    ZNF92 Rooted zinc finger protein 92 (zinc finger protein htf12) (fragment). [swissprot;acc:q03936] 76.1821 78.0464 1.8643
    4207 EXOC4 Divided exocyst complex component sec8. [swissprot;acc:q96a65] 72.5029 74.3099 1.02492

    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/