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 Interaction Map Hugo network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 1551 to 1600 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Interaction Map
    		Hugo
    		network_comparison
    		red
    		green
    194 Rooted eap30 subunit of ell complex. [refseq;acc:nm_007241] High confidence SNF8 1.1486 59.6399 51.9242
    nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] Low confidence NOX3 1.06154 69.9164 74.2188
    195 Measured cyclin g1 (cyclin g). [swissprot;acc:p51959] High confidence CCNG1 1.26743 17738.5 13995.6
    phosphatidylinositol glycan, class b. [refseq;acc:nm_004855] Low confidence PIGB 1.07446 11403 12252.1
    Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] no value 1.0517 211.679 222.623
    huntingtin interacting protein c. [refseq;acc:nm_012272] High confidence PRPF40B 1.13748 227.971 200.417
    Squared septin 2 (nedd5 protein homolog). [swissprot;acc:q15019] Low confidence 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] High confidence SSR4 1.34373 71062.4 95488.9
    Rooted liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] SLC39A6 1.1486 59.6399 51.9242
    nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] Low confidence NOX1 1.06154 69.9166 74.219
    196 Measured natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] 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] High confidence PPP2R5E 1.26742 17738.5 13995.7
    Ranked forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] FOXP4 1.13745 263.215 231.407
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Low confidence GNG12 1.0517 211.679 222.623
    Squared calsyntenin-1 precursor. [swissprot;acc:o94985] High confidence CLSTN1 1.34373 71062.4 95488.9
    sodium/potassium-transporting atpase beta-2 chain (sodium/potassium- dependent atpase beta-2 subunit). [swissprot;acc:p14415] Low confidence ATP1B2 1.10823 52543.2 47411.7
    Rooted f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] CAPZA1 1.06149 68.0822 72.2685
    glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] High confidence GAD2 1.1486 59.6399 51.9242
    197 Measured diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] Low confidence DGKH 1.07336 6519.03 6997.26
    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] High confidence PPP2R5A 1.26742 17738.5 13995.7
    Ranked 60s ribosomal protein l27. [swissprot;acc:p08526] Low confidence RPL27 1.05138 211.912 201.556
    forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] High confidence FOXP1 1.13745 263.215 231.407
    Squared 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] no value 1.34373 71062.4 95488.9
    x/potassium-transporting atpase beta-m chain (x,k-atpase beta-m subunit). [swissprot;acc:q9un42] Low confidence ATP1B4 1.10806 52525.1 47402.9
    Rooted gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] High confidence NAPG 1.1486 59.6399 51.9242
    mitochondrial import inner membrane translocase subunit tim23. [swissprot;acc:o14925] Low confidence TIMM23 1.0613 65.3912 69.4
    198 Measured b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] High confidence BRAF 1.26708 17710.9 13977.7
    diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760] Low confidence DGKD 1.07336 6519.03 6997.26
    Ranked forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] High confidence FOXP3 1.13741 263.191 231.394
    heat-shock 20 kda like-protein p20. [swissprot;acc:o14558] Low confidence HSPB6 1.05123 219.606 208.904
    Squared protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] High confidence PTPRB 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] Low confidence ATP1B3 1.10802 52520.9 47400.8
    Rooted conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] COG5 1.06117 67.1873 71.2973
    glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] High confidence GAD1 1.1486 59.6399 51.9242
    199 Measured prohibitin. [swissprot;acc:p35232] Low confidence PHB 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] High confidence PPP2CA 1.26455 4916.8 3888.18
    Ranked alpha crystallin a chain. [swissprot;acc:p02489] Low confidence CRYAA 1.05119 219.589 208.895
    palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] High confidence EGFL8 1.13729 242.735 276.059
    Squared hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] Low confidence HEYL 1.10778 52187.1 47109.7
    thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] High confidence PRSS16 1.34373 71062.2 95488.6
    Rooted source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] STT3B 1.14842 61.2893 70.3856
    tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] Low confidence TPM4 1.06097 70.8512 75.1709
    200 Measured crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] High confidence BCAR1 1.26315 4808.79 6074.21
    rad50-interacting protein 1. [refseq;acc:nm_021930] Low confidence RINT1 1.07324 6926.74 7434.04
    Ranked alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511] CRYAB 1.05111 219.543 208.868
    egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] High confidence EGFL7 1.1372 242.718 276.018
    Squared bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] Low confidence BRD3 1.10772 54179.7 48910.9
    gk001 protein. [refseq;acc:nm_020198] High confidence CCDC47 1.34373 71062.2 95488.6
    Rooted 60s ribosomal protein l27. [swissprot;acc:p08526] Low confidence RPL27 1.06095 69.691 73.939
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] High confidence STT3A 1.14842 61.2893 70.3856

    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/