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 description Value Type Hugo Interaction Map Filtered network_comparison red green
    Results: HTML CSV LaTeX Showing element 1558 to 1607 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Value Type
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    195 phosphatidylinositol glycan, class b. [refseq;acc:nm_004855] Measured PIGB Low confidence 1.07446 11403 12252.1
    septin 2 (nedd5 protein homolog). [swissprot;acc:q15019] Squared SEPT2 1.10833 58865.4 65242.4
    translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] SSR4 High confidence 1.34373 71062.4 95488.9
    196 calsyntenin-1 precursor. [swissprot;acc:o94985] CLSTN1
    f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Rooted CAPZA1 Low confidence 1.06149 68.0822 72.2685
    forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Ranked FOXP4 High confidence 1.13745 263.215 231.407
    glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Rooted GAD2 1.1486 59.6399 51.9242
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Ranked GNG12 Low confidence 1.0517 211.679 222.623
    natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] Measured SLC11A2 1.07415 6985.66 7503.62
    serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] PPP2R5E High confidence 1.26742 17738.5 13995.7
    sodium/potassium-transporting atpase beta-2 chain (sodium/potassium- dependent atpase beta-2 subunit). [swissprot;acc:p14415] Squared ATP1B2 Low confidence 1.10823 52543.2 47411.7
    197 60s ribosomal protein l27. [swissprot;acc:p08526] Ranked RPL27 1.05138 211.912 201.556
    diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] Measured DGKH 1.07336 6519.03 6997.26
    forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Ranked FOXP1 High confidence 1.13745 263.215 231.407
    gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Rooted NAPG 1.1486 59.6399 51.9242
    mitochondrial import inner membrane translocase subunit tim23. [swissprot;acc:o14925] TIMM23 Low confidence 1.0613 65.3912 69.4
    serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Measured PPP2R5A High confidence 1.26742 17738.5 13995.7
    succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Squared no value 1.34373 71062.4 95488.9
    x/potassium-transporting atpase beta-m chain (x,k-atpase beta-m subunit). [swissprot;acc:q9un42] ATP1B4 Low confidence 1.10806 52525.1 47402.9
    198 b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Measured BRAF High confidence 1.26708 17710.9 13977.7
    conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] Rooted COG5 Low confidence 1.06117 67.1873 71.2973
    diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760] Measured DGKD 1.07336 6519.03 6997.26
    forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Ranked FOXP3 High confidence 1.13741 263.191 231.394
    glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Rooted GAD1 1.1486 59.6399 51.9242
    heat-shock 20 kda like-protein p20. [swissprot;acc:o14558] Ranked HSPB6 Low confidence 1.05123 219.606 208.904
    protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Squared PTPRB High confidence 1.34373 71062.2 95488.6
    sodium/potassium-transporting atpase beta-3 chain (sodium/potassium- dependent atpase beta-3 subunit) (atpb-3). [swissprot;acc:p54709] ATP1B3 Low confidence 1.10802 52520.9 47400.8
    199 alpha crystallin a chain. [swissprot;acc:p02489] Ranked CRYAA 1.05119 219.589 208.895
    hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] Squared HEYL 1.10778 52187.1 47109.7
    palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Ranked EGFL8 High confidence 1.13729 242.735 276.059
    prohibitin. [swissprot;acc:p35232] Measured PHB Low confidence 1.07334 10642 11422.5
    serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] PPP2CA High confidence 1.26455 4916.8 3888.18
    source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Rooted STT3B 1.14842 61.2893 70.3856
    thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Squared PRSS16 1.34373 71062.2 95488.6
    tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] Rooted TPM4 Low confidence 1.06097 70.8512 75.1709
    200 60s ribosomal protein l27. [swissprot;acc:p08526] RPL27 1.06095 69.691 73.939
    alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511] Ranked CRYAB 1.05111 219.543 208.868
    bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] Squared BRD3 1.10772 54179.7 48910.9
    crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Measured BCAR1 High confidence 1.26315 4808.79 6074.21
    egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Ranked EGFL7 1.1372 242.718 276.018
    gk001 protein. [refseq;acc:nm_020198] Squared CCDC47 1.34373 71062.2 95488.6
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Rooted STT3A 1.14842 61.2893 70.3856
    rad50-interacting protein 1. [refseq;acc:nm_021930] Measured RINT1 Low confidence 1.07324 6926.74 7434.04
    201 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] ARAF 1.07323 10392.7 9683.56
    calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Squared CLSTN2 High confidence 1.3436 71033.4 95440.2
    cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Ranked CYC1 Low confidence 1.051 208.591 219.23
    dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Rooted NCBP2L 1.06076 71.1262 75.4476
    dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] DDOST High confidence 1.14842 61.2893 70.3856
    hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] Squared HEY1 Low confidence 1.10771 52176.8 47103.2
    splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Ranked SF4 High confidence 1.13601 240.133 211.382

    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/