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 description Gene Hugo Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 1008 to 1057 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    1008 wd-repeat protein bing4. [swissprot;acc:o15213] WDR46 243.227 235.475 1.03292
    1009 dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] no value 229.116 221.823 1.03288
    1010 peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] CROT 217.523 210.648 1.03264
    1011 retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] RBL2 217.026 210.189 1.03253
    1012 retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] RBL1 217.021 210.185 1.03252
    1013 protein bap28. [swissprot;acc:q9h583] HEATR1 244.312 236.647 1.03239
    1014 apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] AATF 243.045 235.422 1.03238
    1015 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] MAGI1 221.73 228.906 1.03236
    1016 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] KPNA4 217.369 210.561 1.03233
    1017 target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] TOE1 217.365 210.558
    1018 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] KPNA3 217.361 210.554
    1019 tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] TYRL 221.302 214.409 1.03215
    1020 dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] DCT 221.28 1.03205
    1021 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] TYRP1 221.278 1.03204
    1022 cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] CBS 205.632 199.266 1.03195
    1023 transforming protein rhoc (h9). [swissprot;acc:p08134] RHOC
    1024 thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] TST
    1025 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] MPST
    1026 transforming protein rhoa (h12). [swissprot;acc:p06749] RHOA
    1027 succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597] SUCLG1 211.908 218.627 1.03171
    1028 succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [swissprot;acc:q9p2r7] SUCLA2
    1029 dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] DDB1 222.364 215.535 1.03168
    1030 propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] PCCB
    1031 probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] EMG1 242.978 235.518 1.03167
    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] AGPAT2 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] TYR 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] ESRRB 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] MAGI2 221.682 228.68 1.03157
    1036 coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] COPB1 171.341 176.746 1.03155
    1037 thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541] GLRX3 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] no value 186.741 181.041 1.03148
    1039 dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622] DLD 207.719 214.236 1.03137
    1040 t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643] CCT5 163.24 168.359 1.03136
    1041 heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] HNRNPL 186.774 181.099 1.03134
    1042 estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] no value 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] AGPAT3 187.834 182.137 1.03128
    1044 t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] DYNLT3 173.475 178.889 1.03121
    1045 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] FIP1L1 115.817 119.432
    1046 double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] MRE11A 173.475 178.889
    1047 steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] ESRRA 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] AGPAT4 187.96 182.308 1.031
    1049 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] no value 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] HSD17B1
    1051 17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] no value
    1052 retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725] RDH8
    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] PSMA5 207.04 200.84 1.03087
    1054 60s ribosomal protein l21. [swissprot;acc:p46778] no value 223.958 217.263 1.03082
    1055 hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] ASNSD1 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] ATP6V1A
    1057 asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] ASNS

    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/