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 description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1808 to 1857 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		red
    		network_comparison
    		green
    113 VPS33B vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Rooted Subtracted Low confidence 69.4249 5.8215 75.2464
    114 no value cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Measured High confidence 13768.2 2302.2 11466
    myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Squared Divided 19321 1.54043 12542.6
    ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Rooted 80.4705 1.26165 101.526
    ATG12 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Squared Subtracted 67438.6 26741.6 40697
    B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Ranked 229.818 37.447 267.265
    DFFB dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] Rooted Low confidence 61.1174 5.7772 66.8946
    DLGAP1 disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] Ranked Divided 197.779 1.07182 211.983
    GNB5 guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Rooted Subtracted High confidence 40.225 15.5199 24.7051
    KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Ranked Divided 332.874 1.24557 267.246
    MAGEA11 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Measured Low confidence 11285.3 1.0937 10318.5
    MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Ranked Subtracted 58 14 44
    OTC ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] Squared Divided 65896.9 1.14832 75670.5
    PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Measured High confidence 4300.47 1.35048 5807.72
    PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Rooted Low confidence 66.9562 1.08017 72.3243
    SLC16A5 monocarboxylate transporter 6 (mct 6) (mct 5). [swissprot;acc:o15375] Squared Subtracted 62486.3 8239.3 70725.6
    SLC16A7 monocarboxylate transporter 2 (mct 2). [swissprot;acc:o60669] Measured 10346.9 857.9 11204.8
    115 no value pnas-18. [sptrembl;acc:q9bzu3] High confidence 13680.5 2270.9 11409.6
    small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Squared 72886.3 25658.2 98544.5
    CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Divided Low confidence 59004.9 1.14691 51446.9
    DGCR14 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Rooted Subtracted High confidence 21.4476 15.4983 36.9459
    DLGAP4 disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Ranked Divided Low confidence 197.779 1.07182 211.983
    FBXW7 f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Rooted 66.9562 1.08017 72.3243
    HAT1 histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Ranked Subtracted High confidence 277.546 37.085 240.461
    KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Divided 332.874 1.24557 267.246
    LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Rooted Subtracted Low confidence 71.084 5.7592 76.8432
    MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Measured Divided 11285.3 1.0937 10318.5
    MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] High confidence 21185 1.34491 28492
    MYH7B dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Squared 19321 1.54043 12542.6
    SLC16A1 monocarboxylate transporter 1 (mct 1). [swissprot;acc:p53985] Subtracted Low confidence 62462.2 8227.5 70689.7
    SLC16A8 monocarboxylate transporter 3 (mct 3). [swissprot;acc:o95907] Measured 10341.7 856.8 11198.5
    SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Ranked 58 14 44
    SPATA6 spermatogenesis associated 6. [refseq;acc:nm_019073] Rooted Divided High confidence 80.4705 1.26165 101.526
    116 no value hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Measured Low confidence 11285.3 1.0937 10318.5
    testican-3 precursor. [swissprot;acc:q9bq16] Ranked Subtracted 220.395 13.994 234.389
    AMPD2 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Rooted Divided High confidence 80.4705 1.26165 101.526
    FKBP8 38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318] Squared Low confidence 52687.3 1.14667 45948.1
    GATAD2A p66 alpha. [refseq;acc:nm_017660] Subtracted High confidence 81888.8 25582.3 56306.5
    GNB1 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Rooted 40.6302 15.185 25.4452
    GNB3 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Ranked Divided 268.565 1.24545 334.483
    HMG20B high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Subtracted 208.52 36.925 171.595
    Rooted Low confidence 69.0515 5.6978 74.7493
    MYH13 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Squared Divided High confidence 19321 1.54043 12542.6
    PANK1 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Measured 21185 1.34491 28492
    PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Rooted Low confidence 66.9562 1.08017 72.3243
    RGL1 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Measured Subtracted High confidence 13261.9 2244.1 11017.8
    SLC16A7 monocarboxylate transporter 2 (mct 2). [swissprot;acc:o60669] Squared Low confidence 62451.1 8222 70673.1
    SLC7A13 amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817] Measured 6991.78 856.67 7848.45
    VPS18 vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Ranked Divided 204.161 1.07008 190.791
    117 ABRA striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] Subtracted 225.495 13.966 211.529

    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/