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 [...,...].
    Network Comparison Type Rank Gene Value Type description Hugo Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 523 to 572 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    66 Ranked guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] GNA11 High confidence 1.25807 267.136 336.077
    mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] MTUS1 Low confidence 1.10518 221.902 200.783
    Squared melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] MAGEA9 High confidence 1.68808 219048 129762
    septin 10 isoform 1. [refseq;acc:nm_144710] SEPT10 Low confidence 1.26038 74803.9 94281
    Rooted dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] DAB2IP 1.10573 55.8923 61.8016
    glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] PYGL High confidence 1.35128 63.8686 47.2654
    67 Measured beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] ARRB2 1.59177 6475.5 10307.5
    hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] NFU1 Low confidence 1.1318 12176.9 13781.8
    Ranked guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] GNAT2 High confidence 1.25805 267.14 336.075
    retinoblastoma-associated factor 600. [refseq;acc:nm_020765] UBR4 Low confidence 1.10505 165.535 149.799
    Squared melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] MAGEA8 High confidence 1.68808 219048 129762
    septin 6. [swissprot;acc:q14141] SEPT6 Low confidence 1.25751 74378.4 93531.9
    Rooted brachyury protein (t protein). [swissprot;acc:o15178] T 1.10559 61.687 68.2003
    myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] MYO15A High confidence 1.35128 63.8686 47.2654
    68 Measured beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] ARRB1 1.59177 6475.5 10307.5
    putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] UBAC1 Low confidence 1.12932 19498.1 17265.4
    Ranked 60s ribosomal protein l37a. [swissprot;acc:p12751] no value 1.10455 239.692 217.005
    guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] GNAZ High confidence 1.25805 267.139 336.075
    Squared melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] MAGEC1 1.68808 219048 129762
    retinoblastoma-associated factor 600. [refseq;acc:nm_020765] UBR4 Low confidence 1.25653 27909.1 35068.7
    Rooted glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] PYGM High confidence 1.35128 63.8686 47.2654
    ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] RASAL2 Low confidence 1.10514 55.9786 61.8641
    69 Measured amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817] SLC7A13 1.12253 6991.78 7848.45
    spermatogenesis associated 6. [refseq;acc:nm_019073] SPATA6 High confidence 1.59177 6475.5 10307.5
    Ranked guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] GNAT1 1.25805 267.14 336.075
    testis-specific protein tex28. [swissprot;acc:o15482] TEX28P2 Low confidence 1.10425 259.517 235.017
    Squared delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor (ec 1.5.1.12) (p5c dehydrogenase). [swissprot;acc:p30038] ALDH4A1 1.25465 80538.1 64191.7
    melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] MAGEA4 High confidence 1.68808 219048 129762
    Rooted amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] APBA1 Low confidence 1.10405 60.7884 67.1136
    neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] NEUROD2 High confidence 1.33581 27.9136 37.2872
    70 Measured amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] AMPD2 1.59177 6475.5 10307.5
    y+l amino acid transporter 1 (y(+)l-type amino acid transporter 1) (y+lat-1) (y+lat1) (monocyte amino acid permease 2) (mop-2). [swissprot;acc:q9um01] SLC7A7 Low confidence 1.12253 6991.78 7848.45
    Ranked 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] GOSR2 1.10425 259.517 235.017
    guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] GNAI2 High confidence 1.25804 267.142 336.074
    Squared melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] no value 1.68808 219048 129762
    phospholipase a-2-activating protein (plap) (pla2p). [swissprot;acc:q9y263] PLAA Low confidence 1.25465 80538.1 64191.7
    Rooted chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] CHD3 High confidence 1.33581 27.9136 37.2872
    transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] TFDP2 Low confidence 1.10058 61.9982 68.2337
    71 Measured cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] SLC7A11 1.12253 6991.78 7848.45
    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] no value High confidence 1.54716 4556.78 2945.26
    Ranked cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Low confidence 1.10421 230.944 209.149
    guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] GNAI1 High confidence 1.25802 267.144 336.073
    Squared a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] ARAF Low confidence 1.24169 63411.7 51068.8
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] MAGEA10 High confidence 1.68808 219048 129762
    Rooted doc-1 related protein (doc-1r). [swissprot;acc:o75956] CDK2AP2 1.33581 27.9136 37.2872
    tbp-associated factor 2; taf2 rna polymerase ii, tata box binding protein (tbp)-associated factor, 150 kd; tata box binding protein (tbp)-associated factor, rna polymerase ii, b, 150kd; cofactor of initiator function, 150kd subunit. [refseq;acc:nm_003184] TAF2 Low confidence 1.10048 59.6397 65.6325
    72 Measured solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] SLC7A6 1.12253 6991.78 7848.45
    uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] PPP2R2D High confidence 1.54715 4556.79 2945.28
    Ranked guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] GNAI3 1.25802 267.144 336.073
    set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] SMYD2 Low confidence 1.10421 230.944 209.149

    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/