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 Network Comparison Type Gene Hugo Value Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2108 to 2157 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		description
    		red
    		green
    		network_comparison
    1054 Subtracted PSMA5 proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] 207.04 200.84 6.2
    1055 Divided ASNSD1 hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] 219.01 212.468 1.03079
    Subtracted NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] 138.705 132.538 6.167
    1056 Divided ATP6V1A vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606] 219.01 212.468 1.03079
    Subtracted no value methyltransferase like 2. [refseq;acc:nm_018396] 147.211 153.371 6.16
    1057 Divided ASNS asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] 219.01 212.468 1.03079
    Subtracted DYNLT1 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] 147.211 153.371 6.16
    1058 Divided ATXN2L ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] 228.105 221.293 1.03078
    Subtracted FZR1 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] 147.211 153.371 6.16
    1059 Divided no value ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 228.105 221.293 1.03078
    Subtracted PCSK5 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] 147.211 153.371 6.16
    1060 Divided NLK nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] 218.162 211.648 1.03078
    Subtracted SEPT6 septin 6. [swissprot;acc:q14141] 126.604 120.463 6.141
    1061 Divided ERC1 elks protein. [refseq;acc:nm_015064] 218.162 211.648 1.03078
    Subtracted AP3M1 adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2] 217.323 211.185 6.138
    1062 Divided ZNF174 zinc finger protein 174 (aw-1). [swissprot;acc:q15697] 269.963 278.239 1.03066
    Subtracted BRP44 brain protein 44. [swissprot;acc:o95563] 126.215 120.078 6.137
    1063 Divided no value zinc finger imprinted 2. [swissprot;acc:q9nzv7] 269.96 278.232 1.03064
    Subtracted SEPT7 septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] 126.215 120.078 6.137
    1064 Divided ZNF24 zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] 269.955 278.221 1.03062
    Subtracted AP3M2 adapter-related protein complex 3 mu 2 subunit (clathrin coat assembly protein ap47 homolog 2) (clathrin coat associated protein ap47 homolog 2) (golgi adaptor ap-1 47 kda protein homolog 2) (ha1 47 kda subunit homolog 2) (clathrin assembly protein assembly protein complex 1 medium chain homolog 2) (p47b). [swissprot;acc:p53677] 217.315 211.183 6.132
    1065 Divided ZSCAN12 zinc finger protein 305. [swissprot;acc:o43309] 269.954 278.219 1.03062
    Subtracted SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] 125.526 119.402 6.124
    1066 Divided ZNF18 zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022] 269.956 278.223 1.03062
    Subtracted SEPT8 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] 124.434 118.318 6.116
    1067 Divided ZNF215 zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] 269.956 278.223 1.03062
    Subtracted GTPBP3 mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] 213.552 207.463 6.089
    1068 Divided ZNF274 zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] 269.953 278.215 1.03061
    Subtracted NDUFB9 nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] 212.345 206.339 6.006
    1069 Divided ZNF232 zinc finger protein 232. [swissprot;acc:q9uny5] 269.954 278.218 1.03061
    Subtracted DPH1 candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] 229.243 235.246 6.003
    1070 Divided ZNF394 zinc finger protein 99. [refseq;acc:nm_032164] 269.954 278.218 1.03061
    Subtracted GIT2 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] 216.78 222.782 6.002
    1071 Divided no value dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] 231.277 238.356 1.03061
    Subtracted MPHOSPH10 u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] 241.496 235.508 5.988
    1072 Divided ZNF213 zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771] 269.954 278.217 1.03061
    Subtracted PPA1 inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181] 224.307 230.242 5.935
    1073 Divided WBP2 ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] 216.901 210.485 1.03048
    Subtracted PPA2 inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869] 224.307 230.242 5.935
    1074 Divided COPB2 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] 174.387 179.697 1.03045
    Subtracted AIPL1 aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9] 224.307 230.242 5.935
    1075 Divided COPG coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] 174.387 179.697 1.03045
    Subtracted AIP ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170] 224.307 230.242 5.935
    1076 Divided COPZ1 coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] 174.387 179.697 1.03045
    Subtracted ATP2C2 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 209.123 203.208 5.915
    1077 Divided ARCN1 coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] 174.387 179.697 1.03045
    Subtracted TPT1 translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] 218.098 212.209 5.889
    1078 Divided PPIE peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] 174.387 179.697 1.03045
    Subtracted FOXK2 interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] 218.006 212.119 5.887
    1079 Divided COPZ2 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299] 174.387 179.697 1.03045

    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/