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 430 to 479 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		red
    		network_comparison
    		green
    27 NEUROD1 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Squared Divided High confidence 143.692 3.18404 457.521
    PRKRAP1 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Measured Low confidence 3840.85 1.20152 4614.87
    SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Ranked High confidence 58 1.31818 44
    28 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Low confidence 142 1.19718 170
    ATF3 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] High confidence 201.949 1.31416 153.671
    Subtracted Low confidence 203.115 32.558 170.557
    CYP24A1 cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973] Rooted 39.8493 13.085 52.9343
    GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] High confidence 149.165 19.466 129.699
    GNA11 guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Ranked 267.136 68.941 336.077
    GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Rooted Divided 40.3372 1.65967 24.3043
    GNG3 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Measured 1834.36 2.04912 895.194
    GNPDA1 glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Rooted Low confidence 52.3425 1.1617 45.0567
    MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Squared Subtracted High confidence 219048 89286 129762
    MAGED4 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Divided Low confidence 82347.8 1.33073 61881.5
    MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Measured Subtracted 13466.8 1814.4 11652.4
    NDN necdin. [swissprot;acc:q99608] High confidence 23693.7 5430.7 18263
    NEUROD4 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Squared Divided 143.692 3.18404 457.521
    PSCD1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Subtracted Low confidence 93450 21334.6 72115.4
    TOB2 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Measured Divided 3098.94 1.2003 3719.66
    29 ATF3 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Ranked 203.115 1.19089 170.557
    CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Squared High confidence 143.692 3.18404 457.521
    CHRAC1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Ranked Subtracted Low confidence 250.244 32.401 217.843
    CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Rooted Divided 48.8531 1.16077 56.7071
    GNAZ guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Ranked Subtracted High confidence 267.139 68.936 336.075
    GNG8 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Measured Divided 1834.52 2.04858 895.507
    MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Subtracted 23693.7 5430.7 18263
    MAGED2 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 89286 129762
    MAGEE2 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Divided Low confidence 82347.8 1.33073 61881.5
    PPP1R14A protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Rooted High confidence 26.0288 1.65937 43.1914
    PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Ranked 187.458 1.29991 243.678
    PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Squared Subtracted Low confidence 92930.5 21128.1 71802.4
    SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] Measured 13081.2 1791.4 14872.6
    TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Divided 3121.28 1.19818 3739.84
    UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Rooted Subtracted High confidence 210.928 18.763 192.165
    UBR4 retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Low confidence 76.5734 12.051 88.6244
    30 no value 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] Squared 92930 21127.9 71802.1
    melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Divided 82347.8 1.33073 61881.5
    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] Ranked High confidence 187.457 1.29991 243.678
    ATF3 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Rooted Subtracted 60.8022 18.7077 79.5099
    BEST1 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Measured Divided Low confidence 36474.3 1.19288 43509.4
    BOK bcl2-related ovarian killer. [refseq;acc:nm_032515] Ranked 265.638 1.18995 223.235
    CDK2AP1 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 High confidence 143.692 3.18404 457.521
    CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Rooted Low confidence 48.8781 1.16055 56.7253
    GNAT2 guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Ranked Subtracted High confidence 267.14 68.935 336.075
    GNG5 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Measured Divided 1834.59 2.04837 895.633
    MAGEF1 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Subtracted 23693.7 5430.7 18263
    MFAP4 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Rooted Divided 26.0288 1.65937 43.1914
    PIGF phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] Measured Subtracted Low confidence 3278 1780.5 5058.5
    PRKRAP1 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Rooted 44.4168 11.5202 55.937
    SON son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Ranked 255.382 31.844 223.538

    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/