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 [...,...].
    description Rank Gene Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1025 to 1074 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] 1711 HLCS High confidence 218.436 215.553 1.01337
    2150 Low confidence 199.129 195.396 1.0191
    bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) (ec 3.6.1.17) (diadenosine 5',5'''-p1,p4-tetraphosphate asymmetrical hydrolase) (diadenosine tetraphosphatase) (ap4a hydrolase) (ap4aase). [swissprot;acc:p50583] 4100 NUDT2 202.893 200.728 1.01079
    bisphosphoglycerate mutase (ec 5.4.2.4) (2,3-bisphosphoglycerate mutase, erythrocyte) (2,3-bisphosphoglycerate synthase) (bpgm) (ec 5.4.2.1) (ec 3.1.3.13) (bpg-dependent pgam). [swissprot;acc:p07738] 4581 BPGM 202.246 200.737 1.00752
    bladder cancer-associated protein (bladder cancer 10 kda protein) (bc10). [swissprot;acc:o60629] 3287 BLCAP 202.983 199.849 1.01568
    bleomycin hydrolase (ec 3.4.22.40) (blm hydrolase) (bmh) (bh). [swissprot;acc:q13867] 1190 BLMH 202.963 198.378 1.02311
    block 23. [sptrembl;acc:q8nhw5] 1091 no value High confidence 226.205 232.858 1.02941
    3896 Low confidence 202.202 199.673 1.01267
    block of proliferation 1. [swissprot;acc:q14137] 512 BOP1 High confidence 250.794 234.433 1.06979
    1038 Low confidence 201.77 196.996 1.02423
    blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526] 340 BET1L 201.827 194.178 1.03939
    blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 901 no value 201.015 196.054 1.0253
    903
    1930 High confidence 196.964 198.935 1.01001
    1932 196.965 198.936
    blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] 900 RHD Low confidence 201.015 196.054 1.0253
    1928 High confidence 196.964 198.935 1.01001
    bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 1748 no value 215.673 212.971 1.01269
    2256 Low confidence 199.902 196.199 1.01887
    bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] 793 SERPINB10 High confidence 224.244 234.511 1.04578
    3797 Low confidence 202.443 199.787 1.01329
    bombesin receptor subtype-3 (brs-3). [swissprot;acc:p32247] 218 BRS3 199.671 209.654 1.05
    bone morphogenetic protein 1 precursor (ec 3.4.24.19) (bmp-1) (procollagen c-proteinase) (pcp) (mammalian tolloid protein) (mtld). [swissprot;acc:p13497] 2008 BMP1 203.84 199.952 1.01944
    bone morphogenetic protein 4 precursor (bmp-4) (bmp-2b). [swissprot;acc:p12644] 4081 BMP4 195.995 193.854 1.01104
    bone morphogenetic protein 5 precursor (bmp-5). [swissprot;acc:p22003] 2928 BMP5 203.478 200.076 1.017
    3069 High confidence 0.00001 0.00001 1
    bone morphogenetic protein 6 precursor (bmp-6). [swissprot;acc:p22004] 2896 BMP6
    2923 Low confidence 203.481 200.077 1.01701
    bone morphogenetic protein 7 precursor (bmp-7) (osteogenic protein 1) (op-1). [swissprot;acc:p18075] 2943 BMP7 203.455 200.059 1.01697
    3128 High confidence 0.00001 0.00001 1
    bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] 2773 BMP8A
    2910 Low confidence 203.494 200.087 1.01703
    brachyury protein (t protein). [swissprot;acc:o15178] 56 T 224.922 202.592 1.11022
    2040 High confidence 210.586 208.803 1.00854
    brain link protein-1 precursor. [swissprot;acc:q9gzv7] 2642 HAPLN2 Low confidence 203.73 200.174 1.01776
    brain protein 16. [refseq;acc:nm_016458] 1847 no value High confidence 216.811 219.195 1.011
    2180 Low confidence 188.304 184.788 1.01903
    brain protein 44-like protein (hspc040) (cgi-129) (pnas-115). [swissprot;acc:q9y5u8] 1080 BRP44L 196.378 191.803 1.02385
    brain protein 44. [swissprot;acc:o95563] 742 BRP44 High confidence 126.215 120.078 1.05111
    1040 Low confidence 182.902 178.58 1.0242
    branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] 1867 BCAT1 199.922 196.027 1.01987
    2672 High confidence 210.957 210.741 1.00102
    branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] 1877 BCAT2 Low confidence 199.88 195.99 1.01985
    2687 High confidence 210.939 210.755 1.00087
    brca1 associated protein. [refseq;acc:nm_006768] 3161 BRAP 0.00001 0.00001 1
    4538 Low confidence 177.657 176.223 1.00814
    brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] 1752 BARD1 High confidence 216.271 218.991 1.01258
    3479 Low confidence 199.172 196.226 1.01501
    brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] 294 BCCIP High confidence 240.782 265.717 1.10356
    1490 Low confidence 202.583 198.329 1.02145

    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/