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 Network Comparison Type Value Type Hugo description Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 1258 to 1307 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		Hugo
    		description
    		Interaction Map
    		network_comparison
    		red
    		green
    158 Measured MTUS1 mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] Low confidence 1.08416 6434.71 6976.28
    Ranked DNAJC8 dnaj homolog subfamily c member 8 (splicing protein spf31) (hspc315). [swissprot;acc:o75937] 1.05988 219.838 207.417
    GPSM2 mosaic protein lgn. [swissprot;acc:p81274] High confidence 1.19466 249.663 298.263
    Squared SEPT7 septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] 1.40418 89182.8 125229
    WDR33 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Low confidence 1.12381 57732.3 51372.1
    Rooted BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] High confidence 1.17346 56.3507 66.1252
    STRN striatin. [swissprot;acc:o43815] Low confidence 1.06851 66.4354 70.987
    159 Measured BRP44 brain protein 44. [swissprot;acc:o95563] 1.08349 10392.1 11259.7
    NDN necdin. [swissprot;acc:q99608] High confidence 1.29736 23693.7 18263
    Ranked GGNBP2 c3hc4-type zinc finger protein; likely ortholog of mouse dioxin inducible factor 3. [refseq;acc:nm_024835] Low confidence 1.05988 219.838 207.417
    RGS17 regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] High confidence 1.19466 249.663 298.263
    Squared HINT1 histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773] Low confidence 1.12001 22187.9 19810.5
    SEPT6 septin 6. [swissprot;acc:q14141] High confidence 1.40359 88953.6 124854
    Rooted no value rna-binding protein. [refseq;acc:nm_019027] 1.17318 52.7642 61.9019
    transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802] Low confidence 1.06818 65.5823 70.0536
    160 Measured MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] High confidence 1.29736 23693.7 18263
    MTHFR methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] Low confidence 1.08304 10452.8 11320.8
    Ranked APC adenomatous polyposis coli protein (apc protein). [swissprot;acc:p25054] 1.0595 222.31 235.538
    GNAO1 guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] High confidence 1.19466 249.663 298.263
    Squared no value homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 1.40126 173408 242989
    PCSK5 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Low confidence 1.11969 54208.6 48413.8
    Rooted no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] High confidence 1.17318 52.7642 61.9019
    DCHS1 protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0] Low confidence 1.06801 65.7817 70.2555
    161 Measured MAGEF1 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] High confidence 1.29736 23693.7 18263
    SLC16A5 monocarboxylate transporter 6 (mct 6) (mct 5). [swissprot;acc:o15375] Low confidence 1.08298 10351.8 11210.8
    Ranked APC2 adenomatous polyposis coli like. [refseq;acc:nm_005883] 1.0594 222.34 235.547
    RAP1GAP rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] High confidence 1.19466 249.663 298.263
    Squared HOXB4 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 1.40126 173408 242989
    PBLD mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] Low confidence 1.11893 60522.9 67721
    Rooted SLC15A2 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] 1.06801 70.5717 75.371
    SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] High confidence 1.17318 52.7642 61.9019
    162 Measured MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] 1.29736 23693.7 18263
    PSCD1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Low confidence 1.08298 12424.3 11472.3
    Ranked DAD1 defender against cell death 1 (dad-1). [swissprot;acc:p46966] 1.05926 197.99 186.913
    NOSTRIN nostrin. [refseq;acc:nm_052946] High confidence 1.19058 209.299 249.187
    Squared GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Low confidence 1.11854 53479.8 47812.1
    HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] High confidence 1.40126 173408 242989
    Rooted HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 1.17318 52.7642 61.9019
    SEPT8 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Low confidence 1.06796 98.7481 105.459
    163 Measured no value melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] High confidence 1.29736 23693.7 18263
    SLC16A1 monocarboxylate transporter 1 (mct 1). [swissprot;acc:p53985] Low confidence 1.08293 10348.5 11206.7
    Ranked SNF8 eap30 subunit of ell complex. [refseq;acc:nm_007241] High confidence 1.19058 209.299 249.187
    VPS41 vacuolar assembly protein vps41 homolog (s53). [swissprot;acc:p49754] Low confidence 1.05907 202.698 191.393
    Squared no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] High confidence 1.40126 173408 242989
    CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Low confidence 1.11847 56828 50808.5
    Rooted EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] High confidence 1.17285 52.7702 61.8915
    STRN4 striatin 4 (zinedin). [swissprot;acc:q9nrl3] Low confidence 1.06757 66.5155 71.0097
    164 Measured MAGEA9 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] High confidence 1.29736 23693.7 18263
    SLC16A7 monocarboxylate transporter 2 (mct 2). [swissprot;acc:o60669] Low confidence 1.08291 10346.9 11204.8
    Ranked PPM1B protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] 1.05898 196.714 185.758

    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/