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 description Gene Network Comparison Type Hugo Value Type red Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 408 to 457 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    102 rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] RAP1GAP Rooted 47.6504 36.9304 1.29028
    103 cullin homolog 1 (cul-1). [swissprot;acc:q13616] CUL1 Measured 2353.63 3225.65 1.3705
    mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] no value Squared 407289 263351 1.54656
    proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] FOS Rooted 60.8365 77.7233 1.27758
    trophinin. [swissprot;acc:q12816] TRO Ranked 88.2482 110.265 1.24949
    104 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] PSCD1 Squared 407289 263351 1.54656
    homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] HOMER2 Ranked 252.371 202.016 1.24926
    jun dimerization protein. [refseq;acc:nm_130469] no value Rooted 60.8365 77.7233 1.27758
    musashi 2 isoform a. [refseq;acc:nm_138962] MSI2 Measured 4241.57 5810.79 1.36996
    105 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] PSCD2 Squared 407289 263351 1.54656
    fos-related antigen 2. [swissprot;acc:p15408] FOSL2 Rooted 60.8675 77.7168 1.27682
    guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] GNB1 Ranked 266.716 333.165 1.24914
    musashi 1. [refseq;acc:nm_002442] MSI1 Measured 4241.57 5810.79 1.36996
    106 cytohesin 4. [swissprot;acc:q9uia0] PSCD4 Squared 407289 263351 1.54656
    nuclear protein ukp68. [refseq;acc:nm_024824] ZC3H14 Measured 4241.57 5810.79 1.36996
    protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] FOSB Rooted 60.8692 77.7165 1.27678
    ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] COQ7 Ranked 252.329 202.004 1.24913
    107 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] NCBP2 Measured 4266.04 5843.51 1.36977
    cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] PSCD3 Squared 407289 263351 1.54656
    fos-related antigen 1 (fra-1). [swissprot;acc:p15407] FOSL1 Rooted 60.875 77.7152 1.27664
    homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] HOMER1 Ranked 252.309 201.998 1.24907
    108 filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] FLNB Measured 4366.44 5899.76 1.35116
    homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] HOMER3 Ranked 252.296 201.995 1.24902
    myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] no value Squared 19321 12542.6 1.54043
    voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] CACNG2 Rooted 49.2925 62.397 1.26585
    109 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] GNB4 Ranked 266.933 333.281 1.24856
    myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] MYH4 Squared 19321 12542.6 1.54043
    rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] REV1 Measured 4366.44 5899.76 1.35116
    voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] CACNG8 Rooted 49.2923 62.3969 1.26585
    110 deltex 2. [refseq;acc:nm_020892] DTX2 Ranked 333.144 267.393 1.2459
    myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] MYH8 Squared 19321 12542.6 1.54043
    protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] PRMT1 Measured 4366.44 5899.76 1.35116
    voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] CACNG4 Rooted 49.293 62.3973 1.26585
    111 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] DTX1 Ranked 332.925 267.274 1.24563
    myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] MYH2 Squared 19321 12542.6 1.54043
    protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] PRMT8 Measured 4366.44 5899.76 1.35116
    voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] CACNG3 Rooted 49.2923 62.3969 1.26585
    112 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] MYH3 Squared 19321 12542.6 1.54043
    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] PBK Ranked 332.874 267.246 1.24557
    u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] SNRP70 Measured 4366.44 5899.76 1.35116
    voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] CACNG5 Rooted 49.3267 62.4167 1.26537
    113 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] ARRB2 80.4705 101.526 1.26165
    filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] no value Measured 4366.44 5899.76 1.35116
    kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] KHDRBS3 Ranked 332.874 267.246 1.24557
    myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] MYH1 Squared 19321 12542.6 1.54043
    114 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] ARRB1 Rooted 80.4705 101.526 1.26165
    huntingtin interacting protein c. [refseq;acc:nm_012272] PRPF40B Measured 4300.47 5807.72 1.35048
    kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] KHDRBS1 Ranked 332.874 267.246 1.24557
    myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] no value Squared 19321 12542.6 1.54043
    115 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] MRPS17 Measured 21185 28492 1.34491

    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/