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 Hugo description Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 708 to 757 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    89 ICK intestinal cell kinase isoform a; mak-related kinase; serine/threonine protein kinase. [refseq;acc:nm_014920] Measured Low confidence 9623.55 10621.3 1.10368
    MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Ranked High confidence 88.2482 110.265 1.24949
    PPM1B protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Squared Low confidence 69693.1 58164.5 1.19821
    SKP1A s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Rooted High confidence 37.3005 48.4141 1.29795
    STARD7 star-related lipid transfer protein 7 (stard7) (start domain- containing protein 7) (gtt1 protein). [swissprot;acc:q9nqz5] Ranked Low confidence 228.743 210.764 1.0853
    90 no value transforming protein n-ras. [swissprot;acc:p01111] Squared High confidence 105469 64130.2 1.64461
    BEST4 vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Rooted Low confidence 187.325 204.557 1.09199
    BRAP brca1 associated protein. [refseq;acc:nm_006768] Squared 83524.5 69821.2 1.19626
    FBXW7 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] Rooted High confidence 37.3005 48.4141 1.29795
    KCND3 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] Measured 2414.77 1698.75 1.4215
    NDN necdin. [swissprot;acc:q99608] Ranked 88.2482 110.265 1.24949
    TAF2 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] Low confidence 237.567 219.229 1.08365
    VASP vasodilator-stimulated phosphoprotein (vasp). [swissprot;acc:p50552] Measured 12768 11571.4 1.10341
    91 no value ena/vasodilator stimulated phosphoprotein-like protein (ena/vasp-like protein). [swissprot;acc:q9ui08]
    CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Rooted High confidence 37.3005 48.4141 1.29795
    KCND1 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Measured 2416.53 1700.8 1.42082
    KIF23 kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241] Squared Low confidence 57471.1 48463.4 1.18587
    MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Ranked High confidence 88.2482 110.265 1.24949
    OPHN1 oligophrenin 1. [swissprot;acc:o60890] Low confidence 233.837 215.973 1.08271
    PTPRA vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Rooted 69.0723 75.4254 1.09198
    RALGDS ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Squared High confidence 90432.9 56304.2 1.60615
    92 no value nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Rooted Low confidence 186.878 204.057 1.09193
    ARHGAP26 oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Ranked 233.592 215.846 1.08222
    CYLD cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] Squared 57471.1 48463.4 1.18587
    MAGEF1 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Ranked High confidence 88.2482 110.265 1.24949
    NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Measured 4117.67 5801.04 1.40882
    PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Squared 29570.7 18601.8 1.58967
    PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Rooted 37.3005 48.4141 1.29795
    VPS33A vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Measured Low confidence 7297.57 8050.82 1.10322
    93 no value formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] High confidence 4245.52 5942.75 1.39977
    ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Squared 29567 18601.6 1.58949
    BEST2 vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Rooted Low confidence 186.878 204.057 1.09193
    CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] High confidence 37.3005 48.4141 1.29795
    CXorf9 chromosome x open reading frame 9; likely ortholog of mouse sh3 gene sly. [refseq;acc:nm_018990] Squared Low confidence 55143.2 46609.7 1.18308
    DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Ranked 247.334 228.84 1.08082
    MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] High confidence 88.2482 110.265 1.24949
    RBM7 putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Measured Low confidence 4616.06 5091.51 1.103
    94 no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] High confidence 4247.86 5941.88 1.39879
    melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Ranked 88.2482 110.265 1.24949
    CHRAC1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Measured Low confidence 5674.92 6255.18 1.10225
    OPHN1 oligophrenin 1. [swissprot;acc:o60890] Rooted 61.0103 66.5804 1.0913
    RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Ranked 247.087 228.693 1.08043
    RBM15B chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Rooted High confidence 47.6504 36.9304 1.29028
    RGL1 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Squared 84857.8 53402.4 1.58903
    SAMSN1 sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [swissprot;acc:q9nsi8] Low confidence 55150.3 46638.9 1.1825
    95 ARHGAP26 oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Rooted 61.0916 66.6358 1.09075
    CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Measured 4626.46 5098.83 1.1021
    MAGEA9 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Ranked High confidence 88.2482 110.265 1.24949
    PPP1R7 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Squared 256169 162517 1.57626
    RGS19 regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Rooted 47.6504 36.9304 1.29028

    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/