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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 932 to 981 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    233 SLC15A1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Subtracted Low confidence 201.41 191.974 9.436
    234 CHRAC1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Divided High confidence 287.41 256.835 1.11905
    CYP51A1 cytochrome p450 51a1 (ec 1.14.13.70) (cypli) (p450li) (sterol 14-alpha demethylase) (lanosterol 14-alpha demethylase) (ldm) (p450-14dm). [swissprot;acc:q16850] Low confidence 208.851 199.38 1.0475
    DUOX2 dual oxidase 2 precursor; dual oxidase-like domains 2; nicotinamide adenine dinucleotide phosphate oxidase; flavoprotein nadph oxidase; nadph thyroid oxidase 2; nadh/nadph thyroid oxidase p138-tox; nadph oxidase/peroxidase duox2. [refseq;acc:nm_014080] Subtracted 210.504 201.086 9.418
    RPS23 40s ribosomal protein s23. [swissprot;acc:p39028] High confidence 243.944 268.195 24.251
    235 MRPS12 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]
    PAH phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Divided 227.357 254.15 1.11785
    SNRPA u1 small nuclear ribonucleoprotein a (u1 snrnp a protein). [swissprot;acc:p09012] Subtracted Low confidence 202.727 193.31 9.417
    SNRPB2 u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] Divided 202.654 193.53 1.04715
    236 CASK peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] 212.056 202.524 1.04707
    DUOX1 dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] Subtracted 210.487 201.076 9.411
    DUS1L pp3111 protein. [refseq;acc:nm_022156] Divided High confidence 227.357 254.15 1.11785
    RBBP7 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Subtracted 252.644 228.42 24.224
    237 DGAT1 diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] Low confidence 210.443 201.051 9.392
    MRPL3 mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] High confidence 242.011 266.18 24.169
    SIM1 single-minded homolog 1. [swissprot;acc:p81133] Divided Low confidence 212.056 202.524 1.04707
    STX18 syntaxin 18. [swissprot;acc:q9p2w9] High confidence 227.357 254.15 1.11785
    238 no value rd protein. [swissprot;acc:p18615]
    MTA1 metastasis-associated protein mta1. [swissprot;acc:q13330] Subtracted 252.512 228.356 24.156
    NUBP2 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Divided Low confidence 200.699 191.678 1.04706
    TNS1 tensin. [refseq;acc:nm_022648] Subtracted 215.258 205.872 9.386
    239 DUOX2 dual oxidase 2 precursor; dual oxidase-like domains 2; nicotinamide adenine dinucleotide phosphate oxidase; flavoprotein nadph oxidase; nadph thyroid oxidase 2; nadh/nadph thyroid oxidase p138-tox; nadph oxidase/peroxidase duox2. [refseq;acc:nm_014080] Divided 210.504 201.086 1.04684
    GSTO1 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] High confidence 227.357 254.15 1.11785
    NOX5 nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] Subtracted Low confidence 210.415 201.035 9.38
    POLR2A dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] High confidence 243.817 267.962 24.145
    240 no value homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Divided Low confidence 162.755 155.476 1.04682
    AIG1 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] High confidence 227.357 254.15 1.11785
    CYBB cytochrome b-245 heavy chain (p22 phagocyte b-cytochrome) (neutrophil cytochrome b, 91 kda polypeptide) (cgd91-phox) (gp91-phox) (heme binding membrane glycoprotein gp91phox) (cytochrome b(558) beta chain) (superoxide-generating nadph oxidase heavy chain subunit). [swissprot;acc:p04839] Subtracted Low confidence 210.414 201.035 9.379
    RBBP4 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] High confidence 252.39 228.297 24.093
    241 ATP5F1 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Divided 227.357 254.15 1.11785
    CDH1 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Subtracted 241.892 265.96 24.068
    HOXB4 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Divided Low confidence 162.755 155.476 1.04682
    NOX3 nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] Subtracted 210.414 201.035 9.379
    242 no value c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] High confidence 241.892 265.959 24.067
    DNAJC12 j domain containing protein 1. [swissprot;acc:q9ukb3] Divided 227.357 254.15 1.11785
    HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Low confidence 162.755 155.476 1.04682
    WDR92 calcineurin b subunit isoform 1 (protein phosphatase 2b regulatory subunit 1) (protein phosphatase 3 regulatory subunit b alpha isoform 1). [swissprot;acc:p06705] Subtracted 214.887 205.509 9.378
    243 no value 60s ribosomal protein l23a. [swissprot;acc:p29316] High confidence 241.884 265.945 24.061
    homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided Low confidence 162.755 155.476 1.04682
    NOX4 nadph oxidase 4. [refseq;acc:nm_016931] Subtracted 210.413 201.035 9.378
    SNX13 sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] Divided High confidence 227.357 254.15 1.11785
    244 GSTO2 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]
    HOXD4 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Low confidence 162.755 155.476 1.04682
    NOX1 nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] Subtracted 210.413 201.035 9.378
    RPL5 60s ribosomal protein l5. [swissprot;acc:p46777] High confidence 241.899 265.924 24.025
    245 HOXB5 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Divided Low confidence 162.755 155.476 1.04682
    PDSS1 trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Subtracted 211.794 202.482 9.312
    RPL19 60s ribosomal protein l19. [swissprot;acc:p14118] High confidence 240.73 264.729 23.999
    SNRPD3 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Divided 226.109 202.333 1.11751
    246 no value 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Subtracted 243.583 267.528 23.945

    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/