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 description Hugo Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 1425 to 1474 of 66312 in total
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    90 brca1 associated protein. [refseq;acc:nm_006768] BRAP Squared Divided Low confidence 83524.5 69821.2 1.19626
    f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] FBXW7 Rooted High confidence 37.3005 48.4141 1.29795
    leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] SHOC2 Squared Subtracted 105482 64136.9 41345.1
    melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] no value Measured Low confidence 11285.3 10318.5 966.8
    necdin. [swissprot;acc:q99608] NDN Ranked Divided High confidence 88.2482 110.265 1.24949
    neuralized-like. [refseq;acc:nm_004210] NEURL Subtracted Low confidence 232.704 216.996 15.708
    potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] KCND3 Measured Divided High confidence 2414.77 1698.75 1.4215
    prohibitin. [swissprot;acc:p35232] PHB Squared Subtracted Low confidence 73503.9 82930.5 9426.6
    ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] no value Measured High confidence 16071.6 12886.8 3184.8
    regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] RGS20 Ranked 249.663 298.263 48.6
    septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] SEPT8 Rooted Low confidence 98.7481 105.459 6.7109
    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] TAF2 Ranked Divided 237.567 219.229 1.08365
    transcription factor jun-d. [swissprot;acc:p17535] JUND Rooted Subtracted High confidence 63.636 79.6225 15.9865
    transforming protein n-ras. [swissprot;acc:p01111] no value Squared Divided 105469 64130.2 1.64461
    vasodilator-stimulated phosphoprotein (vasp). [swissprot;acc:p50552] VASP Measured Low confidence 12768 11571.4 1.10341
    vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] BEST4 Rooted 187.325 204.557 1.09199
    91 cullin homolog 2 (cul-2). [swissprot;acc:q13617] CUL2 High confidence 37.3005 48.4141 1.29795
    ena/vasodilator stimulated phosphoprotein-like protein (ena/vasp-like protein). [swissprot;acc:q9ui08] no value Measured Low confidence 12768 11571.4 1.10341
    guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] GNA11 Rooted Subtracted High confidence 40.2812 24.3678 15.9134
    kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241] KIF23 Squared Divided Low confidence 57471.1 48463.4 1.18587
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] MAGEA10 Measured Subtracted 11285.3 10318.5 966.8
    melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] MAGED1 Ranked Divided High confidence 88.2482 110.265 1.24949
    mouse mammary turmor virus receptor homolog 1. [refseq;acc:nm_152832] FAM89B Subtracted Low confidence 227.429 211.97 15.459
    oligophrenin 1. [swissprot;acc:o60890] OPHN1 Divided 233.837 215.973 1.08271
    potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] KCND1 Measured High confidence 2416.53 1700.8 1.42082
    ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] RALGDS Squared 90432.9 56304.2 1.60615
    ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] no value Subtracted 105482 64137.2 41344.8
    ras-related protein rab-26. [swissprot;acc:q9ulw5] RAB26 Low confidence 61365.7 52044.8 9320.9
    t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] TBX19 Rooted 61.4851 68.1264 6.6413
    transcription factor lbx1. [swissprot;acc:p52954] LBX1 Ranked High confidence 249.663 298.263 48.6
    transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] HRAS Measured 16070.4 12886 3184.4
    vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] PTPRA Rooted Divided Low confidence 69.0723 75.4254 1.09198
    92 cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] CYLD Squared 57471.1 48463.4 1.18587
    dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] NCBP2L Measured High confidence 4117.67 5801.04 1.40882
    guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] GNAQ Rooted Subtracted 40.2812 24.3679 15.9133
    melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 Measured Low confidence 11285.3 10318.5 966.8
    melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] MAGEF1 Ranked Divided High confidence 88.2482 110.265 1.24949
    metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] PITRM1 Squared 29570.7 18601.8 1.58967
    mosaic protein lgn. [swissprot;acc:p81274] GPSM2 Ranked Subtracted 249.663 298.263 48.6
    nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] no value Rooted Divided Low confidence 186.878 204.057 1.09193
    oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] ARHGAP26 Ranked 233.592 215.846 1.08222
    presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] PSEN1 Rooted High confidence 37.3005 48.4141 1.29795
    septin 10 isoform 1. [refseq;acc:nm_144710] SEPT10 Subtracted Low confidence 98.1106 104.718 6.6074
    transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] E2F1 Ranked 220.497 205.364 15.133
    transforming protein n-ras. [swissprot;acc:p01111] no value Measured High confidence 16069.8 12885.6 3184.2
    transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] HRAS Squared 105473 64132.3 41340.7
    vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] VPS33A Measured Divided Low confidence 7297.57 8050.82 1.10322
    zinc finger protein 216. [swissprot;acc:o76080] ZFAND5 Squared Subtracted 79152.9 69833.1 9319.8
    93 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] ALG1 Divided High confidence 29567 18601.6 1.58949
    chromosome x open reading frame 9; likely ortholog of mouse sh3 gene sly. [refseq;acc:nm_018990] CXorf9 Low confidence 55143.2 46609.7 1.18308

    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/