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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Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 2308 to 2357 of 3206 in total
Rank
description
measured
expected
final
Hugo
2308 DJ718P11.1.2 (NOVEL CLASS II AMINOTRANSFERASE SIMILAR TO SERINE PALMOTYLTRANSFERASE (ISOFORM 2)) (FRAGMENT). [SPTREMBL;Acc:Q9UGB5] 0.0423362 0.19065 0.222062418 no value
2309 ADAPTER-RELATED PROTEIN COMPLEX 3 MU 1 SUBUNIT (MU-ADAPTIN 3A) (AP-3 ADAPTER COMPLEX MU3A SUBUNIT). [SWISSPROT;Acc:Q9Y2T2] 0.162756 0.732966 0.222051227 AP3M1
2310 0.208679 0.939792 0.22204807 DCAKD
2311 DNA POLYMERASE GAMMA SUBUNIT 1 (EC 2.7.7.7) (MITOCHONDRIAL DNA POLYMERASE CATALYTIC SUBUNIT) (POLG-ALPHA). [SWISSPROT;Acc:P54098] 0.0274568 0.123653 0.22204718 POLG
2312 ADAPTER-RELATED PROTEIN COMPLEX 3 MU 2 SUBUNIT (CLATHRIN COAT ASSEMBLY PROTEIN AP47 HOMOLOG 2) (CLATHRIN COAT ASSOCIATED PROTEIN AP47 HOMOLOG 2) (GOLGI ADAPTOR AP-1 47 KDA PROTEIN HOMOLOG 2) (HA1 47 KDA SUBUNIT HOMOLOG 2) (CLATHRIN ASSEMBLY PROTEIN ASSEMB 0.183942 0.828397 0.22204571 AP3M2
2313 EXOSOME COMPLEX EXONUCLEASE RRP41 (EC 3.1.13.-) (RIBOSOMAL RNA PROCESSING PROTEIN 41) (P12A). [SWISSPROT;Acc:Q9NPD3] 0.271627 1.22344 0.222019061 EXOSC4
2314 EXOSOME COMPLEX EXONUCLEASE RRP46 (EC 3.1.13.-) (RIBOSOMAL RNA PROCESSING PROTEIN 46) (P12B) (CHRONIC MYELOGENOUS LEUKEMIA TUMOR ANTIGEN 28). [SWISSPROT;Acc:Q9NQT4] EXOSC5
2315 EXOSOME COMPLEX EXONUCLEASE RRP4 (EC 3.1.13.-) (RIBOSOMAL RNA PROCESSING PROTEIN 4). [SWISSPROT;Acc:Q13868] EXOSC2
2316 EXOSOME COMPLEX EXONUCLEASE RRP40 (EC 3.1.13.-) (RIBOSOMAL RNA PROCESSING PROTEIN 40) (P10) (CGI-102). [SWISSPROT;Acc:Q9NQT5] EXOSC3
2317 PHOSPHOMANNOMUTASE 1 (EC 5.4.2.8) (PMM 1) (PMMH-22). [SWISSPROT;Acc:Q92871] 0.146657 0.660778 0.221945949 PMM1
2318 PHOSPHOMANNOMUTASE 2 (EC 5.4.2.8) (PMM 2). [SWISSPROT;Acc:O15305] 0.18235 0.82204 0.221826189 PMM2
2319 LEUKOCYTE ELASTASE INHIBITOR (LEI) (MONOCYTE/NEUTROPHIL ELASTASE INHIBITOR) (M/NEI) (EI). [SWISSPROT;Acc:P30740] 0.0244744 0.110346 0.221796893 SERPINB1
2320 MASPIN PRECURSOR (PROTEASE INHIBITOR 5). [SWISSPROT;Acc:P36952] 0.0193287 0.0871461 0.2217965 no value
2321 CYTOPLASMIC ANTIPROTEINASE 3 (CAP3) (CAP-3) (PROTEASE INHIBITOR 9) (SERPIN B9). [SWISSPROT;Acc:P50453] 0.0200935 0.0905944 0.22179627 SERPINB9
2322 BOMAPIN (PROTEASE INHIBITOR 10) (SERPIN B10). [SWISSPROT;Acc:P48595] 0.0196713 0.088691 0.221795898 SERPINB10
2323 40S RIBOSOMAL PROTEIN S21. [SWISSPROT;Acc:P35265] 0.187278 0.844371 0.221795869 RPS21
2324 CYTOPLASMIC ANTIPROTEINASE 2 (CAP2) (CAP-2) (PROTEASE INHIBITOR 8) (SERPIN B8). [SWISSPROT;Acc:P50452] 0.0199772 0.0900703 0.221795642 no value
2325 40S RIBOSOMAL PROTEIN SA (P40) (34/67 KDA LAMININ RECEPTOR) (COLON CARCINOMA LAMININ-BINDING PROTEIN) (NEM/1CHD4) (MULTIDRUG RESISTANCE- ASSOCIATED PROTEIN MGR1-AG). [SWISSPROT;Acc:P08865] 0.410038 1.84872 0.221795621
2326 SERPIN B11. [SWISSPROT;Acc:Q96P15] 0.0194204 0.0875599 0.221795594
2327 PLACENTAL THROMBIN INHIBITOR (CYTOPLASMIC ANTIPROTEINASE) (CAP) (PROTEASE INHIBITOR 6) (PI-6). [SWISSPROT;Acc:P35237] 0.0199527 0.0899599 0.221795489 SERPINB6
2328 PLASMINOGEN ACTIVATOR INHIBITOR-2 PRECURSOR (PAI-2) (PLACENTAL PLASMINOGEN ACTIVATOR INHIBITOR) (MONOCYTE ARG-SERPIN) (UROKINASE INHIBITOR). [SWISSPROT;Acc:P05120] 0.0198854 0.0896565 0.221795408 SERPINB8
2329 CANDIDATE TUMOR SUPPRESSOR IN OVARIAN CANCER 2. [RefSeq;Acc:NM_080822] 0.322756 1.45734 0.221469252 DPH1
2330 RIBOSOMAL PROTEIN S27-LIKE PROTEIN; 40S RIBOSOMAL PROTEIN S27 ISOFORM. [RefSeq;Acc:NM_015920] 0.221494 1.00105 0.221261675 RPS27L
2331 40S RIBOSOMAL PROTEIN S27 (METALLOPAN-STIMULIN 1) (MPS-1). [SWISSPROT;Acc:P42677] 0.228054 1.0307 0.221261279 no value
2332 TRNA ISOPENTENYLPYROPHOSPHATE TRANSFERASE. [RefSeq;Acc:NM_017646] 0.316686 1.4315 0.221226685 TRIT1
2333 SERINE/THREONINE PROTEIN PHOSPHATASE PP1-ALPHA 1 CATALYTIC SUBUNIT (EC 3.1.3.16) (PP-1A). [SWISSPROT;Acc:P08129] 0.634044 2.86607 0.221224185 PPP1CA
2334 RIBOSOME BIOGENESIS REGULATORY PROTEIN HOMOLOG. [SWISSPROT;Acc:Q15050] 0.0322443 0.145754 0.221224117 RRS1
2335 ADENOSYLHOMOCYSTEINASE (EC 3.3.1.1) (S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE) (ADOHCYASE). [SWISSPROT;Acc:P23526] 0.133936 0.605534 0.221186589 AHCY
2336 0.0295892 0.133775 0.22118632 C1orf50
2337 0.256113 1.15814 0.221141658 D2HGDH
2338 WERNER HELICASE INTERACTING PROTEIN ISOFORM 1; PUTATIVE HELICASE RUVBL; WERNER HELICASE INTERACTING PROTEIN. [RefSeq;Acc:NM_020135] 0.215454 0.975402 0.220887388 WRNIP1
2339 "6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING (EC 1.1.1.44). [SWISSPROT;Acc:P52209]" 0.0670488 0.303687 0.220782582 PGD
2340 TYPE 1 PROTEIN PHOSPHATASE INHIBITOR. [RefSeq;Acc:NM_025210] 0.0612127 0.27731 0.220737442 PPP1R2P9
2341 ARGINYL-TRNA SYNTHETASE-LIKE; ARGININE-TRNA LIGASE. [RefSeq;Acc:NM_020320] 0.21385 0.968873 0.220720363 RARS2
2342 PROTEIN PHOSPHATASE INHIBITOR 2 (IPP-2). [SWISSPROT;Acc:P41236] 0.0820717 0.371844 0.220715408 PPP1R2
2343 MEIOTIC RECOMBINATION PROTEIN DMC1/LIM15 HOMOLOG. [SWISSPROT;Acc:Q14565] 0.108234 0.490411 0.220700596 DMC1
2344 "2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.2.4.4) (BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 COMPONENT ALPHA CHAIN) (BCKDH E1-ALPHA). [SWISSPROT;Acc:P12694]" 0.0287655 0.130409 0.220579101 TMEM91
2345 "PYRUVATE DEHYDROGENASE E1 COMPONENT BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.2.4.1) (PDHE1-B). [SWISSPROT;Acc:P11177]" 0.804341 3.6465 0.220578911 PDHB
2346 THIOREDOXIN DOMAIN CONTAINING; THIOREDOXIN-RELATED TRANSMEMBRANE PROTEIN; THIOREDOXIN DOMAIN-CONTAINING. [RefSeq;Acc:NM_030755] 0.0366305 0.166118 0.220508915 TXNDC1
2347 0.1385 0.628094 0.220508395 no value
2348 TRANSCRIPTION INITIATION FACTOR TFIID 70 KDA SUBUNIT (TAFII-70) (TAFII-80) (TAFII80). [SWISSPROT;Acc:P49848] 0.391086 1.77434 0.220412097 TAF6
2349 0.0640044 0.290417 0.220387925 PIH1D2
2350 0.0498274 0.22609 0.220387456 SLIT1
2351 SERINE--PYRUVATE AMINOTRANSFERASE (EC 2.6.1.51) (SPT) (ALANINE-- GLYOXYLATE AMINOTRANSFERASE) (EC 2.6.1.44) (AGT). [SWISSPROT;Acc:P21549] 0.143655 0.651843 0.220382822 AGXT
2352 UPSTREAM STIMULATORY FACTOR 1 (MAJOR LATE TRANSCRIPTION FACTOR 1). [SWISSPROT;Acc:P22415] 0.0867894 0.39382 0.220378345 USF1
2353 BIFUNCTIONAL AMINOACYL-TRNA SYNTHETASE [INCLUDES: GLUTAMYL-TRNA SYNTHETASE (EC 6.1.1.17) (GLUTAMATE--TRNA LIGASE); PROLYL-TRNA SYNTHETASE (EC 6.1.1.15) (PROLINE--TRNA LIGASE)]. [SWISSPROT;Acc:P07814] 0.337714 1.5325 0.220368026 EPRS
2354 UPSTREAM STIMULATORY FACTOR 2 (UPSTREAM TRANSCRIPTION FACTOR 2) (FOS-INTERACTING PROTEIN) (FIP) (MAJOR LATE TRANSCRIPTION FACTOR 2). [SWISSPROT;Acc:Q15853] 0.0736246 0.334101 0.220366296 USF2
2355 MITOCHONDRIAL 28S RIBOSOMAL PROTEIN S2 (MRP-S2) (CGI-91). [SWISSPROT;Acc:Q9Y399] 0.437521 1.98545 0.220363646 MRPS2
2356 ZINC FINGER PROTEIN GLI1 (GLIOMA-ASSOCIATED ONCOGENE) (ONCOGENE GLI). [SWISSPROT;Acc:P08151] 0.0254221 0.115399 0.220297403 GLI1
2357 ZINC FINGER PROTEIN GLI2 (TAX HELPER PROTEIN). [SWISSPROT;Acc:P10070] GLI2

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/