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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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 Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1025 to 1074 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
red
green
network_comparison
1025 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] MPST 205.632 199.266 1.03195
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
1058 ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] ATXN2L 228.105 221.293 1.03078
1059 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] no value
1060 nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] NLK 218.162 211.648
1061 elks protein. [refseq;acc:nm_015064] ERC1
1062 zinc finger protein 174 (aw-1). [swissprot;acc:q15697] ZNF174 269.963 278.239 1.03066
1063 zinc finger imprinted 2. [swissprot;acc:q9nzv7] no value 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] ZNF24 269.955 278.221 1.03062
1065 zinc finger protein 305. [swissprot;acc:o43309] ZSCAN12 269.954 278.219
1066 zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022] ZNF18 269.956 278.223
1067 zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] ZNF215
1068 zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] ZNF274 269.953 278.215 1.03061
1069 zinc finger protein 232. [swissprot;acc:q9uny5] ZNF232 269.954 278.218
1070 zinc finger protein 99. [refseq;acc:nm_032164] ZNF394
1071 dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] no value 231.277 238.356
1072 zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771] ZNF213 269.954 278.217
1073 ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] WBP2 216.901 210.485 1.03048
1074 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] COPB2 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/