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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2500 to 2549 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    625 HTRA2 Rooted serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] 59.6678 64.3767 1.07892
    626 AHCYL1 Measured putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] 6228.39 7013.19 1.126
    GABRA2 Squared gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] 32192.8 37967.1 1.17937
    GABRE Ranked gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 214.256 202.14 1.05994
    HTRA3 Rooted probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 59.6673 64.3742 1.07889
    627 GABRA6 Squared gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] 32192.8 37967.1 1.17937
    HTRA4 Rooted probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] 59.6674 64.3747 1.07889
    JMJD6 Ranked phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 214.256 202.139 1.05994
    KIAA0430 Measured limkain b1. [refseq;acc:nm_019081] 6228.39 7013.19 1.126
    628 no value putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2]
    GABRA1 Ranked gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] 214.256 202.14 1.05994
    GABRG2 Squared gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] 32192.6 37966.9 1.17937
    HTRA1 Rooted serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] 59.6661 64.3692 1.07882
    629 no value Squared interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] 32192.5 37966.8 1.17937
    CREG1 Measured cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] 6228.39 7013.19 1.126
    GABRA3 Ranked gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] 214.256 202.14 1.05994
    SYN3 Rooted synapsin iii. [swissprot;acc:o14994] 60.0129 64.7371 1.07872
    630 no value aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
    DLGAP3 Measured disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] 6228.39 7013.19 1.126
    GABRA4 Squared gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] 32192.8 37967.1 1.17937
    NDUFA6 Ranked nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] 214.256 202.141 1.05993
    631 GABRE Squared gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 32192.8 37967.1 1.17937
    HEY1 Rooted 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] 60.0129 64.7371 1.07872
    KNG1 Measured kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] 6228.39 7013.19 1.126
    PDXDC1 Ranked similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] 214.256 202.141 1.05993
    632 no value Measured disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] 6228.39 7013.19 1.126
    ABLIM2 Rooted actin binding lim protein 2. [refseq;acc:nm_032432] 60.0129 64.7371 1.07872
    HOXD9 Ranked homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] 214.254 202.166 1.05979
    JMJD6 Squared phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 32192.5 37966.8 1.17937
    633 AARS Ranked alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] 234.106 248.104 1.05979
    FTL Measured ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] 6228.39 7013.19 1.126
    GABRA1 Squared gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] 32192.8 37967.2 1.17937
    HEYL Rooted hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] 60.0129 64.7371 1.07872
    634 no value Ranked dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 226.523 213.786 1.05958
    DLGAP4 Measured disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] 6228.39 7013.19 1.126
    GABRA3 Squared gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] 32192.8 37967.1 1.17937
    SYN2 Rooted synapsin ii. [swissprot;acc:q92777] 60.0129 64.7371 1.07872
    635 FTHL17 Measured ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] 6228.97 7013.53 1.12595
    HOXC9 Squared homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] 32189.9 37963.6 1.17936
    MRRF Rooted mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] 60.0129 64.7371 1.07872
    RPL37 Ranked 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] 228.639 242.258 1.05957
    636 HOXB9 Squared homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] 32187.7 37961 1.17936
    PEX5 Rooted peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] 60.0129 64.7371 1.07872
    PSMA5 Measured proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] 5713.41 6432.92 1.12593
    SFRS1 Ranked splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955] 228.639 242.258 1.05957
    637 HEY2 Rooted hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] 60.0129 64.7371 1.07872
    HOXA9 Squared homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] 32188.2 37961.6 1.17936
    NME2P1 Measured putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] 7756.51 8731.76 1.12573
    PPAT Ranked amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203] 228.639 242.258 1.05957
    638 HES1 Rooted transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] 60.0129 64.7371 1.07872

    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/