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 1114 to 1163 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		Value Type
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    70 PLAA Divided Squared phospholipase a-2-activating protein (plap) (pla2p). [swissprot;acc:q9y263] Low confidence 80538.1 64191.7 1.25465
    PPP2R1B Subtracted Ranked serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] High confidence 188.688 242.742 54.054
    PPP2R5E Measured serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] 17738.5 13995.7 3742.8
    RAF1 Squared raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Low confidence 63404.8 51065.9 12338.9
    SEPT1 Measured septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 10499 11515.8 1016.8
    SLC7A7 Divided 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] 6991.78 7848.45 1.12253
    TFDP2 Rooted transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] 61.9982 68.2337 1.10058
    71 no value Measured 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] High confidence 4556.78 2945.26 1.54716
    Ranked cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Low confidence 230.944 209.149 1.10421
    ARAF Squared a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 63411.7 51068.8 1.24169
    ATG3 Subtracted apg3p; pc3-96 protein. [refseq;acc:nm_022488] High confidence 129597 73157.5 56439.5
    CDK2AP2 Divided Rooted doc-1 related protein (doc-1r). [swissprot;acc:o75956] 27.9136 37.2872 1.33581
    GNAI1 Ranked guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] 267.144 336.073 1.25802
    JUND Subtracted transcription factor jun-d. [swissprot;acc:p17535] Low confidence 202.709 183.361 19.348
    KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] High confidence 265.686 319.651 53.965
    MAGEA10 Divided Squared melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] 219048 129762 1.68808
    NIPSNAP1 Subtracted Rooted nipsnap1 protein. [swissprot;acc:q9bpw8] Low confidence 55.133 62.1073 6.9743
    PANK1 Squared pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 52120.9 64447.1 12326.2
    PPP2R5A Measured serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] High confidence 17738.5 13995.7 3742.8
    PYGM Rooted glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 63.8686 47.2654 16.6032
    SLC7A11 Divided Measured cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] Low confidence 6991.78 7848.45 1.12253
    TAF2 Rooted 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] 59.6397 65.6325 1.10048
    UFC1 Subtracted Measured protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 5339.5 6352.4 1012.9
    72 no value Rooted homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 101.348 108.302 6.954
    BRAF Measured b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] High confidence 17710.9 13977.7 3733.2
    C10orf83 Squared 44050 protein. [refseq;acc:nm_178832] 148058 99628.4 48429.6
    DTX2 Rooted deltex 2. [refseq;acc:nm_020892] 27.634 43.9629 16.3289
    GNAI3 Divided Ranked guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] 267.144 336.073 1.25802
    KCNIP4 Subtracted potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 265.639 319.546 53.907
    MAGEB4 Divided Squared melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] 219048 129762 1.68808
    MAK Subtracted Measured serine/threonine-protein kinase mak (ec 2.7.1.-) (male germ cell- associated kinase). [swissprot;acc:p20794] Low confidence 9631.47 10633 1001.53
    MTUS1 Divided Rooted mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] 63.1259 69.4305 1.09987
    NEUROD6 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] High confidence 27.9136 37.2872 1.33581
    PPP2R2D Measured uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 4556.79 2945.28 1.54715
    RAF1 Squared raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Low confidence 63404.8 51065.9 1.24163
    SLC7A6 Measured solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] 6991.78 7848.45 1.12253
    SMYD2 Ranked set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] 230.944 209.149 1.10421
    TFDP2 Subtracted transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] 227.623 208.281 19.342
    TP53I3 Squared tumor protein p53 inducible protein 3; quinone oxidoreductase homolog; p53-induced gene 3 protein. [refseq;acc:nm_004881] 70019.5 82296.2 12276.7
    73 CPN2 Divided carboxypeptidase n 83 kda chain (carboxypeptidase n regulatory subunit) (fragment). [swissprot;acc:p22792] 63279.6 51013.1 1.24046
    DTX1 Subtracted Rooted deltex homolog 1; hdx-1. [refseq;acc:nm_004416] High confidence 27.7078 44.017 16.3092
    EIF4B Divided Measured eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] Low confidence 6991.78 7848.45 1.12253
    GP5 Subtracted Squared platelet glycoprotein v precursor (gpv) (cd42d). [swissprot;acc:p40197] 63279.9 51013.3 12266.6
    HOXB4 Rooted homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 101.348 108.302 6.954
    ICK Measured intestinal cell kinase isoform a; mak-related kinase; serine/threonine protein kinase. [refseq;acc:nm_014920] 9623.55 10621.3 997.75
    JPH3 Divided Ranked junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] High confidence 288 362 1.25694
    JUNB Subtracted transcription factor jun-b. [swissprot;acc:p17275] Low confidence 202.728 183.388 19.34
    KCNIP2 kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] High confidence 265.632 319.531 53.899
    MAGED2 Divided Squared melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] 219048 129762 1.68808
    NEUROD1 Rooted neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 27.9136 37.2872 1.33581

    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/