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 [...,...].
    Gene Rank description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 901 to 950 of 77072 in total
    Rank
    		description
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		Filtered
    		red
    		green
    		network_comparison
    29 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] Rooted Subtracted High confidence 0 11.3774 1.80368 9.57372
    cytochrome c oxidase polypeptide viic, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p15954] Measured Low confidence 20505.7 21088.5 582.8
    cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Squared 1 92930.5 71802.4 21128.1
    cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Rooted Divided 48.8531 56.7071 1.16077
    galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Squared Subtracted High confidence 0 72128.6 64272.5 7856.1
    glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Ranked Low confidence 11761 15924 4163
    Rooted Divided 11.9583 6.85565 1.7443
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Measured High confidence 1 1834.52 895.507 2.04858
    guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Ranked Subtracted 267.139 336.075 68.936
    hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Squared Divided Low confidence 0 3.41692 0.355148 9.62112
    hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 1 82347.8 61881.5 1.33073
    melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Measured 0 105.5 35.5 2.97183
    melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Subtracted High confidence 1 23693.7 18263 5430.7
    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] Squared 219048 129762 89286
    microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Rooted Divided 0 17.7955 7.34614 2.42243
    phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Ranked 7395 11625 1.57201
    pnas-129. [sptrembl;acc:q9bxv8] Rooted Subtracted Low confidence 16.4276 9.246 7.1816
    potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Measured Divided High confidence 111.278 434.911 3.90833
    potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Squared 5.18438 141.427 27.2794
    protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Rooted 1 26.0288 43.1914 1.65937
    putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Subtracted 210.928 192.165 18.763
    regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] Measured 0 3248.95 2399.76 849.19
    retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Rooted Low confidence 1 76.5734 88.6244 12.051
    septin 10 isoform 1. [refseq;acc:nm_144710] Measured 13081.2 14872.6 1791.4
    solute carrier family 12 (potassium/chloride transporters), member 9; cation-chloride cotransporter-interacting protein. [refseq;acc:nm_020246] Ranked Divided 0 12129.6 8687.07 1.39628
    sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Squared Subtracted 8202.27 15317.3 7115.03
    tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Measured Divided 1 3121.28 3739.84 1.19818
    uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Ranked High confidence 187.458 243.678 1.29991
    30 alpha 2 globin. [refseq;acc:nm_000517] Low confidence 0 11486.2 15987.1 1.39185
    bcl2-related ovarian killer. [refseq;acc:nm_032515] 1 265.638 223.235 1.18995
    bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Measured 36474.3 43509.4 1.19288
    beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Ranked High confidence 0 7395 11625 1.57201
    cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Measured Subtracted 3265.25 4102.97 837.72
    cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Rooted 1 60.8022 79.5099 18.7077
    cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Squared Divided 143.692 457.521 3.18404
    cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Rooted Low confidence 48.8781 56.7253 1.16055
    dystrophin. [swissprot;acc:p11532] Measured High confidence 0 427.217 111.739 3.82335
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 1 1834.59 895.633 2.04837
    guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Ranked Subtracted 267.14 336.075 68.935
    homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Rooted 0 0 9.43398 9.43398
    lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Ranked 13730.5 8257 5473.5
    Squared Low confidence 1082.48 7964.87 6882.39
    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] 1 92930 71802.1 21127.9
    melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Measured Divided 0 105.5 35.5 2.97183
    melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Squared 1 82347.8 61881.5 1.33073
    melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 0 3.41692 0.355148 9.62112
    melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Measured Subtracted High confidence 1 23693.7 18263 5430.7
    microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Rooted Divided 26.0288 43.1914 1.65937
    phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] Measured Subtracted Low confidence 3278 5058.5 1780.5
    potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Squared Divided High confidence 0 6.25494 141.944 22.6931

    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
    - 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/