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 green red network_comparison
    Results: HTML CSV LaTeX Showing element 1051 to 1100 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		green
    		red
    		network_comparison
    1051 no value 17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] 217.998 211.449 1.03097
    1052 RDH8 retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725]
    1053 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] 200.84 207.04 1.03087
    1054 no value 60s ribosomal protein l21. [swissprot;acc:p46778] 217.263 223.958 1.03082
    1055 ASNSD1 hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] 212.468 219.01 1.03079
    1056 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]
    1057 ASNS asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]
    1058 ATXN2L ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] 221.293 228.105 1.03078
    1059 no value ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]
    1060 NLK nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] 211.648 218.162
    1061 ERC1 elks protein. [refseq;acc:nm_015064]
    1062 ZNF174 zinc finger protein 174 (aw-1). [swissprot;acc:q15697] 278.239 269.963 1.03066
    1063 no value zinc finger imprinted 2. [swissprot;acc:q9nzv7] 278.232 269.96 1.03064
    1064 ZNF24 zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] 278.221 269.955 1.03062
    1065 ZSCAN12 zinc finger protein 305. [swissprot;acc:o43309] 278.219 269.954
    1066 ZNF18 zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022] 278.223 269.956
    1067 ZNF215 zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58]
    1068 ZNF274 zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] 278.215 269.953 1.03061
    1069 ZNF232 zinc finger protein 232. [swissprot;acc:q9uny5] 278.218 269.954
    1070 ZNF394 zinc finger protein 99. [refseq;acc:nm_032164]
    1071 no value dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] 238.356 231.277
    1072 ZNF213 zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771] 278.217 269.954
    1073 WBP2 ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] 210.485 216.901 1.03048
    1074 COPB2 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] 179.697 174.387 1.03045
    1075 COPG coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678]
    1076 COPZ1 coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3]
    1077 ARCN1 coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444]
    1078 PPIE peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9]
    1079 COPZ2 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299]
    1080 ZNF444 zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] 278.093 269.896 1.03037
    1081 FAU 40s ribosomal protein s30. [swissprot;acc:q05472] 216.875 223.44 1.03027
    1082 PLEKHF2 phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] 213.685 220.118 1.03011
    1083 SRD5A1 3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405]
    1084 SRD5A2 3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213]
    1085 DKC1 dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] 237.864 231.007 1.02968
    1086 no value similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 243.679 236.679 1.02958
    1087 zinc finger protein 277. [swissprot;acc:q9nrm2]
    1088 ANXA11 annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995] 213.378 219.673 1.0295
    1089 CSTF3 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 125.004 121.428 1.02945
    1090 no value similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] 232.88 226.218
    1091 block 23. [sptrembl;acc:q8nhw5] 232.858 226.205 1.02941
    1092 RPLP0 60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] 232.855 226.203
    1093 COPA coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] 182.647 177.432 1.02939
    1094 ANXA7 annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] 213.385 219.655 1.02938
    1095 GTPBP3 mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] 207.463 213.552 1.02935
    1096 NDUFB9 nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] 206.339 212.345 1.02911
    1097 ATP2C2 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 203.208 209.123
    1098 AP3M1 adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2] 211.185 217.323 1.02906
    1099 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] 211.183 217.315 1.02904
    1100 ATP2C1 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] 203.183 209.052 1.02889

    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/