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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expected Rank measured Gene description Hugo final
Results: HTML CSV LaTeX Showing element 1802 to 1851 of 3206 in total
expected
Rank
measured
description
Hugo
final
0.63809 431 0.176985 ARGININE-GLUTAMIC ACID DIPEPTIDE (RE) REPEATS; ATROPHIN 1-LIKE; ARGININE GLUTAMIC ACID DIPEPTIDE RE REPEATS. [RefSeq;Acc:NM_012102] RERE 0.277366829
432 "2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.2.4.4) (BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 COMPONENT BETA CHAIN) (BCKDH E1-BETA). [SWISSPROT;Acc:P21953]" BCKDHB
433 POLYPYRIMIDINE TRACT-BINDING PROTEIN 1 (PTB) (HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN I) (HNRNP I) (57 KDA RNA-BINDING PROTEIN PPTB-1). [SWISSPROT;Acc:P26599] PTBP1
434 MEMBRANE-ASSOCIATED NUCLEIC ACID BINDING PROTEIN. [RefSeq;Acc:NM_018835] RC3H2
0.639129 2277 0.142292 "PEPTIDE CHAIN RELEASE FACTOR 1, MITOCHONDRIAL PRECURSOR (MRF-1). [SWISSPROT;Acc:O75570]" MTRF1 0.222634241
0.639469 3072 0.0659913 DAB2 INTERACTING PROTEIN; NGAP-LIKE PROTEIN; DOC-2/DAB2 INTERACTIVE PROTEIN. [RefSeq;Acc:NM_032552] DAB2IP 0.103197028
0.640129 1402 0.15625 FBXO28 0.244091425
0.640229 677 0.170317 SERINE/THREONINE-PROTEIN KINASE PLK (EC 2.7.1.-) (PLK-1) (SERINE- THREONINE PROTEIN KINASE 13) (STPK13). [SWISSPROT;Acc:P53350] PLK1 0.266025125
0.641454 1368 0.157068 HISTONE H3.1 (H3/A) (H3/C) (H3/D) (H3/F) (H3/H) (H3/I) (H3/J) (H3/K) (H3/L). [SWISSPROT;Acc:P16106] no value 0.244862453
0.641462 366 0.179445 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN H3 (HNRNP H3) (HNRNP 2H9). [SWISSPROT;Acc:P31942] HNRPH3 0.279743773
0.641812 1615 0.153801 C20orf11 0.239635594
0.64258 1609 0.154124 KATANIN P60 SUBUNIT A 1. [RefSeq;Acc:NM_007044] KATNA1 0.239851847
0.643016 1789 0.15115 PREFOLDIN SUBUNIT 2 (HSPC231). [SWISSPROT;Acc:Q9UHV9] PFDN2 0.235064135
0.64312 1636 0.153821 MITOTIC CHECKPOINT PROTEIN BUB3. [SWISSPROT;Acc:O43684] BUB3 0.239179313
0.643957 2874 0.121508 "ENOYL-COA HYDRATASE, MITOCHONDRIAL PRECURSOR (EC 4.2.1.17) (SHORT CHAIN ENOYL-COA HYDRATASE) (SCEH) (ENOYL-COA HYDRATASE 1). [SWISSPROT;Acc:P30084]" ECHS1 0.188689617
0.645054 2701 0.133976 METAXIN 1. [SWISSPROT;Acc:Q13505] MTX1 0.20769734
0.646308 2472 0.139984 CUEDC2 0.216590233
0.6464 2226 0.145091 PMS1 PROTEIN HOMOLOG 2 (DNA MISMATCH REPAIR PROTEIN PMS2). [SWISSPROT;Acc:P54278] PMS2 0.224460087
0.646587 1035 0.163807 CATHEPSIN L2 PRECURSOR (EC 3.4.22.43) (CATHEPSIN V) (CATHEPSIN U). [SWISSPROT;Acc:O60911] CTSL2 0.253341004
0.647682 3066 0.0670742 MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B (MAP1A/MAP1B LC3 B) (MAP1A/1B LIGHT CHAIN 3 B). [SWISSPROT;Acc:Q9GZQ8] MAP1LC3B 0.103560389
0.648176 655 0.173445 EUKARYOTIC TRANSLATION INITIATION FACTOR 4E (EIF-4E) (EIF4E) (MRNA CAP-BINDING PROTEIN) (EIF-4F 25 KDA SUBUNIT). [SWISSPROT;Acc:P06730] EIF4E 0.267589358
0.648338 3188 0.0241928 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 14A; 17-KDA PKC-POTENTIATED INHIBITORY PROTEIN OF PP1. [RefSeq;Acc:NM_033256]" PPP1R14A 0.037315104
0.648924 918 0.167384 VACUOLAR PROTEIN SORTING 11 (HVPS11) (PP3476). [SWISSPROT;Acc:Q9H270] VPS11 0.257940837
0.649418 2694 0.13519 "STEROID HORMONE RECEPTOR ERR1 (ESTROGEN-RELATED RECEPTOR, ALPHA) (ERR-ALPHA) (ESTROGEN RECEPTOR-LIKE 1). [SWISSPROT;Acc:P11474]" ESRRA 0.208171009
0.649575 932 0.167087 LIMKAIN BETA 2. [RefSeq;Acc:NM_025140] CCDC92 0.257225109
0.649583 3194 0.0239451 CHMP4C 0.036862264
0.649898 106 0.23886 WISKOTT-ALDRICH SYNDROME PROTEIN INTERACTING PROTEIN (WASP INTERACTING PROTEIN) (PRPL-2 PROTEIN). [SWISSPROT;Acc:O43516] WIPF1 0.367534598
0.650054 3112 0.0597428 CYTOHESIN 1 (SEC7 HOMOLOG B2-1). [SWISSPROT;Acc:Q15438] PSCD1 0.091904365
0.651828 1195 0.161995 "COP9 COMPLEX SUBUNIT 4; LIKELY ORTHOLOG OF MOUSE COP9 (CONSTITUTIVE PHOTOMORPHOGENIC), SUBUNIT 4 (ARABIDOPSIS); COP9 (CONSTITUTIVE PHOTOMORPHOGENIC, ARABIDOPSIS, HOMOLOG) SUBUNIT 4. [RefSeq;Acc:NM_016129]" COPS4 0.248524151
0.651843 2351 0.143655 SERINE--PYRUVATE AMINOTRANSFERASE (EC 2.6.1.51) (SPT) (ALANINE-- GLYOXYLATE AMINOTRANSFERASE) (EC 2.6.1.44) (AGT). [SWISSPROT;Acc:P21549] AGXT 0.220382822
0.65236 3053 0.0691801 BA305P22.3 (BREAST CARCINOMA AMPLIFIED SEQUENCE 4). [SPTREMBL;Acc:Q8NDY6] BHLHB4 0.106045895
0.65249 1294 0.160447 RBMX2 0.245899554
0.652691 19 0.310118 E2A-PBX1-ASSOCIATED PROTEIN; PUTATIVE 47 KDA PROTEIN. [RefSeq;Acc:NM_020140] ANKS1B 0.475137546
0.652697 1721 0.154828 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 9 (26S PROTEASOME REGULATORY SUBUNIT P27). [SWISSPROT;Acc:O00233] PSMD9 0.237212673
0.654219 2086 0.149641 "GLUTAMATE DEHYDROGENASE 2, MITOCHONDRIAL PRECURSOR (EC 1.4.1.3) (GDH). [SWISSPROT;Acc:P49448]" GLUD2 0.228732275
2087 "GLUTAMATE DEHYDROGENASE 1, MITOCHONDRIAL PRECURSOR (EC 1.4.1.3) (GDH). [SWISSPROT;Acc:P00367]" GLUDP5
0.654349 1821 0.153292 DNA FRAGMENTATION FACTOR 40 KDA SUBUNIT (EC 3.-.-.-) (DFF-40) (CASPASE-ACTIVATED DEOXYRIBONUCLEASE) (CASPASE-ACTIVATED DNASE) (CAD) (CASPASE-ACTIVATED NUCLEASE) (CPAN). [SWISSPROT;Acc:O76075] DFFB 0.234266424
0.654499 2024 0.150764 TRANSKETOLASE (EC 2.2.1.1) (TK). [SWISSPROT;Acc:P29401] TKT 0.230350237
0.655122 2053 0.150581 "SUCCINATE DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.3.5.1) (FP) (FLAVOPROTEIN SUBUNIT OF COMPLEX II). [SWISSPROT;Acc:P31040]" SDHA 0.229851844
0.656717 149 0.230683 "KH DOMAIN CONTAINING, RNA BINDING, SIGNAL TRANSDUCTION ASSOCIATED 3; SAM68-LIKE PHOSPHOTYROSINE PROTEIN, T-STAR. [RefSeq;Acc:NM_006558]" KHDRBS3 0.351266984
0.657687 2431 0.143043 FIBULIN-1 PRECURSOR. [SWISSPROT;Acc:P23142] FBLN1 0.217494036
0.658159 271 0.201492 NADH-UBIQUINONE OXIDOREDUCTASE B22 SUBUNIT (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-B22) (CI-B22). [SWISSPROT;Acc:Q9Y6M9] NDUFB9 0.306144868
0.659693 440 0.182551 GLUTATHIONE S-TRANSFERASE THETA 2 (EC 2.5.1.18) (GST CLASS-THETA). [SWISSPROT;Acc:P30712] GSTT2B 0.276721142
0.660778 2317 0.146657 PHOSPHOMANNOMUTASE 1 (EC 5.4.2.8) (PMM 1) (PMMH-22). [SWISSPROT;Acc:Q92871] PMM1 0.221945949
0.66093 1444 0.16091 GLUTAMYL TRNA SYNTHETASE. [SPTREMBL;Acc:O14563] EARS2 0.243459973
0.662751 2286 0.147358 MAP3K7IP3 0.222342931
0.663781 1784 0.156153 "C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC (C1-THF SYNTHASE) [INCLUDES: METHYLENETETRAHYDROFOLATE DEHYDROGENASE (EC 1.5.1.5); METHENYLTETRAHYDROFOLATE CYCLOHYDROLASE (EC 3.5.4.9); FORMYLTETRAHYDROFOLATE SYNTHETASE (EC 6.3.4.3)]. [SWISSPROT;Acc:P115" MTHFD1 0.23524777
0.664457 1875 0.154668 GOLGI COMPLEX ASSOCIATED PROTEIN 1; GOLGI RESIDENT PROTEIN GCP60; PERIPHERIAL BENZODIAZEPINE RECEPTOR ASSOCIATED PROTEIN; GOLGI PHOSPHOPROTEIN 1; PBR ASSOCIATED PROTEIN; PKA (RIALPHA)-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_022735] ACBD3 0.232773528
0.665535 1520 0.161284 PAN3 0.242337368
0.668251 1088 0.168157 "ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 1 SUBUNIT (MU-ADAPTIN 1) (ADAPTOR PROTEIN COMPLEX AP-1 MU-1 SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN MU-1 SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN ASSEMBLY PROTEIN COMPLEX 1 MEDIUM CHAIN 1) (CLATHRIN COAT ASSEMBLY PROTEIN A" AP1M1 0.251637484

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/