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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Gene measured expected Rank description Hugo final
Results: HTML CSV LaTeX Showing element 651 to 700 of 3206 in total
measured
expected
Rank
description
Hugo
final
0.0424223 0.169541 1148 GBP PROTEIN ISOFORM A. [RefSeq;Acc:NM_017870] TMEM132A 0.250218531
0.0424293 0.159817 698 15 KDA SELENOPROTEIN PRECURSOR. [SWISSPROT;Acc:O60613] no value 0.265486775
0.0424937 0.171305 1219 WDR55 0.248058726
0.042516 0.151058 357 no value 0.281454805
0.0425806 0.168127 1045 TMEM87A 0.253264496
0.0426192 1.78381 3203 RAS-RELATED GTP BINDING B SHORT ISOFORM; GTP-BINDING PROTEIN RAGB. [RefSeq;Acc:NM_006064] RRAGB 0.023892231
0.0426374 0.158312 595 "SPECTRIN BETA CHAIN, BRAIN 1 (SPECTRIN, NON-ERYTHROID BETA CHAIN 1) (BETA-II SPECTRIN) (FODRIN BETA CHAIN). [SWISSPROT;Acc:Q01082]" SPTBN1 0.26932513
0.0427222 0.141553 281 RETINAL PIGMENT EPITHELIUM-SPECIFIC PROTEIN 65KDA; RETINAL PIGMENT EPITHELIUM-SPECIFIC PROTEIN (65KD); RETINITIS PIGMENTOSA 20 (AUTOSOMAL RECESSIVE). [RefSeq;Acc:NM_000329] RPE65 0.301810629
0.04274 0.180308 1734 EAP30 SUBUNIT OF ELL COMPLEX. [RefSeq;Acc:NM_007241] SNF8 0.237038845
0.0429379 0.169867 1051 RNA (GUANINE-7-) METHYLTRANSFERASE. [RefSeq;Acc:NM_003799] RNMT 0.252773641
0.0429558 0.142328 294 "BETA-CAROTENE DIOXYGENASE 2; PUTATIVE B,B-CAROTENE-9',10'-DIOXYGENASE. [RefSeq;Acc:NM_031938]" no value 0.301808499
0.0429594 0.169952 1050 CALNEXIN PRECURSOR (MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I ANTIGEN-BINDING PROTEIN P88) (P90) (IP90). [SWISSPROT;Acc:P27824] CANX 0.252773724
0.0430845 0.223156 2837 THYMUS-SPECIFIC SERINE PROTEASE PRECURSOR (EC 3.4.-.-). [SWISSPROT;Acc:Q9NQE7] PRSS16 0.193068974
0.0431276 0.223379 2835 "SUCCINATE DEHYDROGENASE [UBIQUINONE] CYTOCHROME B SMALL SUBUNIT, MITOCHONDRIAL PRECURSOR (CYBS) (SUCCINATE-UBIQUINONE REDUCTASE MEMBRANE ANCHOR SUBUNIT) (QPS2) (CII-4) (SUCCINATE DEHYDROGENASE COMPLEX SUBUNIT D) (SUCCINATE-UBIQUINONE OXIDOREDUCTASE CYTOCH" no value 0.193069178
0.0431799 0.15929 543 LRRC4C 0.27107728
0.0433512 0.201854 2523 STAR-RELATED LIPID TRANSFER PROTEIN 4 (STARD4) (START DOMAIN- CONTAINING PROTEIN 4). [SWISSPROT;Acc:Q96DR4] STARD4 0.214765127
0.0434449 0.193087 2213 LRRC48 0.225001683
0.0434669 0.206986 2628 MITOGEN-ACTIVATED PROTEIN KINASE 14 (EC 2.7.1.37) (MITOGEN-ACTIVATED PROTEIN KINASE P38ALPHA) (MAP KINASE P38ALPHA) (CYTOKINE SUPPRESSIVE ANTI-INFLAMMATORY DRUG BINDING PROTEIN) (CSAID BINDING PROTEIN) (CSBP) (MAX-INTERACTING PROTEIN 2) (MAP KINASE MXI2) MAPK14 0.209999227
0.0435693 0.20874 2676 N-ACETYLGALACTOSAMINE KINASE (EC 2.7.1.-) (GALNAC KINASE) (GALACTOKINASE 2). [SWISSPROT;Acc:Q01415] GALK2 0.208725208
0.0436424 0.163636 672 no value 0.266704148
0.0436706 0.144696 290 NXNL1 0.301809311
0.0436957 0.203458 2522 no value 0.21476521
0.0437393 0.144924 293 PHENYLETHANOLAMINE N-METHYLTRANSFERASE (EC 2.1.1.28) (PNMTASE) (NORADRENALINE N-METHYLTRANSFERASE). [SWISSPROT;Acc:P11086] PNMT 0.301808534
0.0438075 0.415448 3056 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(Z), ALPHA SUBUNIT (G(X) ALPHA CHAIN) (GZ-ALPHA). [SWISSPROT;Acc:P19086]" GNAZ 0.10544641
0.043878 0.204307 2524 STAR-RELATED LIPID TRANSFER PROTEIN 6 (STARD6) (START DOMAIN- CONTAINING PROTEIN 6). [SWISSPROT;Acc:P59095] STARD6 0.214765035
0.0439174 0.172112 989 CPG BINDING PROTEIN (PROTEIN CONTAINING PHD FINGER AND CXXC DOMAIN 1). [SWISSPROT;Acc:Q9P0U4] CXXC1 0.255167565
0.0439474 0.179636 1379 "SUPPRESSOR OF VAR1, 3-LIKE 1. [RefSeq;Acc:NM_003171]" SUPV3L1 0.244646953
0.0439645 0.158002 402 CENTAURIN GAMMA 1. [SWISSPROT;Acc:Q99490] CENTG1 0.278252807
0.0439756 0.197784 2298 HOMEOBOX PROTEIN DLX-3. [SWISSPROT;Acc:O60479] DLX3 0.222341544
0.0439931 0.74486 3171 PROLINE SYNTHETASE CO-TRANSCRIBED BACTERIAL HOMOLOG PROTEIN. [SWISSPROT;Acc:O94903] PROSC 0.05906224
0.0440508 0.183648 1608 KATANIN P80 SUBUNIT B 1; KATANIN (80 KDA); KATANIN P80 (WD40-CONTAINING) SUBUNIT B 1. [RefSeq;Acc:NM_005886] KATNB1 0.239865395
0.0441291 0.166122 694 "ATP-BINDING CASSETTE, SUB-FAMILY D, MEMBER 3 (70 KDA PEROXISOMAL MEMBRANE PROTEIN) (PMP70). [SWISSPROT;Acc:P28288]" ABCD3 0.26564272
0.0441578 0.169647 862 PYROXD1 0.260292254
863 "RABAPTIN, RAB GTPASE BINDING EFFECTOR PROTEIN 1; RABAPTIN-5; NEUROCRESCIN. [RefSeq;Acc:NM_004703]" RABEP1
0.0442218 0.200737 2359 GASTRICSIN PRECURSOR (EC 3.4.23.3) (PEPSINOGEN C). [SWISSPROT;Acc:P20142] PGC 0.220297205
0.0442559 0.183485 1561 ARRDC4 0.241196283
0.0442587 0.15995 443 PEROXISOMAL N1-ACETYL-SPERMINE/SPERMIDINE OXIDASE. [RefSeq;Acc:NM_152911] PAOX 0.276703345
0.0443146 0.199308 2290 HOMEOBOX PROTEIN DLX-5. [SWISSPROT;Acc:P56178] DLX5 0.222342304
0.044407 0.421142 3057 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1 SUBUNIT (TRANSDUCIN ALPHA-1 CHAIN). [SWISSPROT;Acc:P11488]" GNAT1 0.105444244
0.0444208 0.444481 3079 PLASMA CARBOXYPEPTIDASE B2 ISOFORM A PREPROPROTEIN; CARBOXYPEPTIDASE U; THROMBIN-ACTIVATABLE FIBRINOLYSIS INHIBITOR; CARBOXYPEPTIDASE B-LIKE PROTEIN; THROMBIN-ACTIVABLE FIBRINOLYSIS INHIBITOR. [RefSeq;Acc:NM_001872] CPB2 0.09993858
0.0444453 0.352603 3004 ENDO-BETA-N-ACETYLGLUCOSAMINIDASE. [RefSeq;Acc:NM_022759] no value 0.126049126
0.0444465 0.161679 468 GTP-BINDING PROTEIN ERA HOMOLOG (HERA) (FRAGMENT). [SWISSPROT;Acc:O75616] ERAL1 0.274905832
0.0444473 0.483626 3113 CYTOHESIN 4. [SWISSPROT;Acc:Q9UIA0] PSCD4 0.091904281
0.0444669 0.162108 478 "SOLUTE CARRIER FAMILY 23, MEMBER 1 (SODIUM-DEPENDENT VITAMIN C TRANSPORTER 1) (HSVCT1) (NA(+)/L-ASCORBIC ACID TRANSPORTER 1) (YOLK SAC PERMEASE-LIKE MOLECULE 3). [SWISSPROT;Acc:Q9UHI7]" SLC23A1 0.274304168
479 SHC TRANSFORMING PROTEIN. [SWISSPROT;Acc:P29353] SHC1
0.0445191 0.177917 1147 TMEM132E 0.250223981
0.0446932 0.423859 3058 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-2 SUBUNIT (TRANSDUCIN ALPHA-2 CHAIN). [SWISSPROT;Acc:P19087]" GNAT2 0.105443556
0.0447647 0.119758 103 "SELENIDE,WATER DIKINASE 2 (EC 2.7.9.3) (SELENOPHOSPHATE SYNTHETASE 2) (SELENIUM DONOR PROTEIN 2). [SWISSPROT;Acc:Q99611]" SEPHS2 0.373792983
0.044904 0.188793 1700 no value 0.237847802
0.0451789 0.452071 3080 MAST CELL CARBOXYPEPTIDASE A PRECURSOR (EC 3.4.17.1) (MC-CPA) (CARBOXYPEPTIDASE A3). [SWISSPROT;Acc:P15088] CPA3 0.09993762

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/