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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1032 to 1081 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		red
    		green
    		network_comparison
    1032 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] 186.664 180.943 1.03162
    1033 tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] 221.183 214.406 1.03161
    1034 steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] 186.551 180.837 1.0316
    1035 atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301] 221.682 228.68 1.03157
    1036 coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] 171.341 176.746 1.03155
    1037 thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541] 228.412 235.609 1.03151
    1038 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] 186.741 181.041 1.03148
    1039 dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622] 207.719 214.236 1.03137
    1040 t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643] 163.24 168.359 1.03136
    1041 heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] 186.774 181.099 1.03134
    1042 estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] 186.799 181.127 1.03132
    1043 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] 187.834 182.137 1.03128
    1044 t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] 173.475 178.889 1.03121
    1045 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 115.817 119.432
    1046 double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] 173.475 178.889
    1047 steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] 187.022 181.391 1.03104
    1048 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] 187.96 182.308 1.031
    1049 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] 211.449 217.998 1.03097
    1050 estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061]
    1051 17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034]
    1052 retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725]
    1053 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 1.03087
    1054 60s ribosomal protein l21. [swissprot;acc:p46778] 223.958 217.263 1.03082
    1055 hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] 219.01 212.468 1.03079
    1056 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 asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]
    1058 ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] 228.105 221.293 1.03078
    1059 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]
    1060 nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] 218.162 211.648
    1061 elks protein. [refseq;acc:nm_015064]
    1062 zinc finger protein 174 (aw-1). [swissprot;acc:q15697] 269.963 278.239 1.03066
    1063 zinc finger imprinted 2. [swissprot;acc:q9nzv7] 269.96 278.232 1.03064
    1064 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
    1065 zinc finger protein 305. [swissprot;acc:o43309] 269.954 278.219
    1066 zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022] 269.956 278.223
    1067 zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58]
    1068 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
    1069 zinc finger protein 232. [swissprot;acc:q9uny5] 269.954 278.218
    1070 zinc finger protein 99. [refseq;acc:nm_032164]
    1071 dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] 231.277 238.356
    1072 zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771] 269.954 278.217
    1073 ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] 216.901 210.485 1.03048
    1074 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] 174.387 179.697 1.03045
    1075 coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678]
    1076 coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3]
    1077 coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444]
    1078 peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9]
    1079 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299]
    1080 zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] 269.896 278.093 1.03037
    1081 40s ribosomal protein s30. [swissprot;acc:q05472] 223.44 216.875 1.03027

    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
    - 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/