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 212 to 261 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    27 Ranked mitochondrial solute carrier protein. [refseq;acc:nm_145305] SLC25A43 High confidence 1.31818 58 44
    Squared ena/vasodilator stimulated phosphoprotein-like protein (ena/vasp-like protein). [swissprot;acc:q9ui08] no value Low confidence 1.33526 97360.9 72915.2
    neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] NEUROD1 High confidence 3.18404 143.692 457.521
    Rooted glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335] GNPDA2 Low confidence 1.1617 52.3425 45.0567
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] no value High confidence 1.66015 40.3364 24.2968
    28 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] GNG3 2.04912 1834.36 895.194
    tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] TOB2 Low confidence 1.2003 3098.94 3719.66
    Ranked atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] no value 1.19718 142 170
    cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] ATF3 High confidence 1.31416 201.949 153.671
    Squared melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] MAGED4 Low confidence 1.33073 82347.8 61881.5
    neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] NEUROD4 High confidence 3.18404 143.692 457.521
    Rooted glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] GNPDA1 Low confidence 1.1617 52.3425 45.0567
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] GNG11 High confidence 1.65967 40.3372 24.3043
    29 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] GNG8 2.04858 1834.52 895.507
    tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] TOB1 Low confidence 1.19818 3121.28 3739.84
    Ranked cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] ATF3 1.19089 203.115 170.557
    uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] PPP2R2D High confidence 1.29991 187.458 243.678
    Squared chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] CHD5 3.18404 143.692 457.521
    hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] MAGEE2 Low confidence 1.33073 82347.8 61881.5
    Rooted cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] CPEB3 1.16077 48.8531 56.7071
    protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] PPP1R14A High confidence 1.65937 26.0288 43.1914
    30 Measured bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] BEST1 Low confidence 1.19288 36474.3 43509.4
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] GNG5 High confidence 2.04837 1834.59 895.633
    Ranked bcl2-related ovarian killer. [refseq;acc:nm_032515] BOK Low confidence 1.18995 265.638 223.235
    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 1.29991 187.457 243.678
    Squared 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] CDK2AP1 3.18404 143.692 457.521
    melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] no value Low confidence 1.33073 82347.8 61881.5
    Rooted cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] CPEB4 1.16055 48.8781 56.7253
    microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] MFAP4 High confidence 1.65937 26.0288 43.1914
    31 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] GNG10 2.04827 1834.63 895.697
    vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] BEST4 Low confidence 1.19287 36469.3 43503.3
    Ranked deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] DNASE2B 1.17568 57.395 48.8186
    serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] PPP2R2B High confidence 1.2999 187.458 243.677
    Squared beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] ARRB2 2.53372 9924.76 25146.6
    melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] MAGEA11 Low confidence 1.33073 82347.8 61881.5
    Rooted 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] MRPS17 1.1597 145.551 168.796
    protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] PPP1R14D High confidence 1.65937 26.0288 43.1914
    32 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] no value 2.04793 1834.73 895.893
    nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence 1.19275 36360.3 43368.8
    Ranked protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] PRKRAP1 1.17505 273.188 232.49
    serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] PPP2R2C High confidence 1.29985 187.462 243.673
    Squared beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] ARRB1 2.53372 9924.76 25146.6
    melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] MAGEA2B Low confidence 1.33073 82347.8 61881.5
    Rooted ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] FCN2 High confidence 1.65937 26.0288 43.1914
    mitochondrial solute carrier protein. [refseq;acc:nm_145305] SLC25A43 Low confidence 1.1597 145.551 168.796
    33 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] GNG11 High confidence 2.04611 1835.3 896.972
    vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] BEST2 Low confidence 1.19275 36360.3 43368.8
    Ranked dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] MAP2K4 1.17068 210.241 246.125
    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] PPP2R1B High confidence 1.28647 188.688 242.742
    Squared hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] no value Low confidence 1.33073 82347.8 61881.5

    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/