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