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 Rank expected description measured Hugo final
Results: HTML CSV LaTeX Showing element 2301 to 2350 of 3206 in total
Rank
expected
description
measured
Hugo
final
2301 0.469849 P10-BINDING PROTEIN. [RefSeq;Acc:NM_024491] 0.10445 CEP70 0.222305464
2302 1.04193 DNA DIRECTED RNA POLYMERASE II POLYPEPTIDE J-RELATED GENE ISOFORM 3; RPB11B1ALPHA PROTEIN; RPB11B1BETA; DNA-DIRECTED RNA POLYMERASE II SUBUNIT 11. [RefSeq;Acc:NM_032959] 0.231616 no value 0.222295164
2303 1.0479 DNA DIRECTED RNA POLYMERASE II POLYPEPTIDE J-RELATED GENE ISOFORM 1; RPB11B1ALPHA PROTEIN; RPB11B1BETA; DNA-DIRECTED RNA POLYMERASE II SUBUNIT 11. [RefSeq;Acc:NM_145325] 0.232938 0.222290295
2304 0.235868 SERINE PALMITOYLTRANSFERASE 2 (EC 2.3.1.50) (LONG CHAIN BASE BIOSYNTHESIS PROTEIN 2) (LCB 2) (SERINE-PALMITOYL-COA TRANSFERASE 2) (SPT 2). [SWISSPROT;Acc:O15270] 0.0524219 SPTLC2 0.222251005
2305 0.875357 GLUTAMATE CARBOXYPEPTIDASE-LIKE PROTEIN 2 PRECURSOR. [SWISSPROT;Acc:Q96KN2] 0.194519 CNDP1 0.222216764
2306 1.14298 0.25396 no value 0.222191114
2307 2.62976 "GOLGI REASSEMBLY STACKING PROTEIN 2; GOLGI REASSEMBLY STACKING PROTEIN 2, 55 KDA. [RefSeq;Acc:NM_015530]" 0.584026 GORASP2 0.222083384
2308 0.19065 DJ718P11.1.2 (NOVEL CLASS II AMINOTRANSFERASE SIMILAR TO SERINE PALMOTYLTRANSFERASE (ISOFORM 2)) (FRAGMENT). [SPTREMBL;Acc:Q9UGB5] 0.0423362 no value 0.222062418
2309 0.732966 ADAPTER-RELATED PROTEIN COMPLEX 3 MU 1 SUBUNIT (MU-ADAPTIN 3A) (AP-3 ADAPTER COMPLEX MU3A SUBUNIT). [SWISSPROT;Acc:Q9Y2T2] 0.162756 AP3M1 0.222051227
2310 0.939792 0.208679 DCAKD 0.22204807
2311 0.123653 DNA POLYMERASE GAMMA SUBUNIT 1 (EC 2.7.7.7) (MITOCHONDRIAL DNA POLYMERASE CATALYTIC SUBUNIT) (POLG-ALPHA). [SWISSPROT;Acc:P54098] 0.0274568 POLG 0.22204718
2312 0.828397 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 AP3M2 0.22204571
2313 1.22344 EXOSOME COMPLEX EXONUCLEASE RRP41 (EC 3.1.13.-) (RIBOSOMAL RNA PROCESSING PROTEIN 41) (P12A). [SWISSPROT;Acc:Q9NPD3] 0.271627 EXOSC4 0.222019061
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 0.660778 PHOSPHOMANNOMUTASE 1 (EC 5.4.2.8) (PMM 1) (PMMH-22). [SWISSPROT;Acc:Q92871] 0.146657 PMM1 0.221945949
2318 0.82204 PHOSPHOMANNOMUTASE 2 (EC 5.4.2.8) (PMM 2). [SWISSPROT;Acc:O15305] 0.18235 PMM2 0.221826189
2319 0.110346 LEUKOCYTE ELASTASE INHIBITOR (LEI) (MONOCYTE/NEUTROPHIL ELASTASE INHIBITOR) (M/NEI) (EI). [SWISSPROT;Acc:P30740] 0.0244744 SERPINB1 0.221796893
2320 0.0871461 MASPIN PRECURSOR (PROTEASE INHIBITOR 5). [SWISSPROT;Acc:P36952] 0.0193287 no value 0.2217965
2321 0.0905944 CYTOPLASMIC ANTIPROTEINASE 3 (CAP3) (CAP-3) (PROTEASE INHIBITOR 9) (SERPIN B9). [SWISSPROT;Acc:P50453] 0.0200935 SERPINB9 0.22179627
2322 0.088691 BOMAPIN (PROTEASE INHIBITOR 10) (SERPIN B10). [SWISSPROT;Acc:P48595] 0.0196713 SERPINB10 0.221795898
2323 0.844371 40S RIBOSOMAL PROTEIN S21. [SWISSPROT;Acc:P35265] 0.187278 RPS21 0.221795869
2324 0.0900703 CYTOPLASMIC ANTIPROTEINASE 2 (CAP2) (CAP-2) (PROTEASE INHIBITOR 8) (SERPIN B8). [SWISSPROT;Acc:P50452] 0.0199772 no value 0.221795642
2325 1.84872 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 0.221795621
2326 0.0875599 SERPIN B11. [SWISSPROT;Acc:Q96P15] 0.0194204 0.221795594
2327 0.0899599 PLACENTAL THROMBIN INHIBITOR (CYTOPLASMIC ANTIPROTEINASE) (CAP) (PROTEASE INHIBITOR 6) (PI-6). [SWISSPROT;Acc:P35237] 0.0199527 SERPINB6 0.221795489
2328 0.0896565 PLASMINOGEN ACTIVATOR INHIBITOR-2 PRECURSOR (PAI-2) (PLACENTAL PLASMINOGEN ACTIVATOR INHIBITOR) (MONOCYTE ARG-SERPIN) (UROKINASE INHIBITOR). [SWISSPROT;Acc:P05120] 0.0198854 SERPINB8 0.221795408
2329 1.45734 CANDIDATE TUMOR SUPPRESSOR IN OVARIAN CANCER 2. [RefSeq;Acc:NM_080822] 0.322756 DPH1 0.221469252
2330 1.00105 RIBOSOMAL PROTEIN S27-LIKE PROTEIN; 40S RIBOSOMAL PROTEIN S27 ISOFORM. [RefSeq;Acc:NM_015920] 0.221494 RPS27L 0.221261675
2331 1.0307 40S RIBOSOMAL PROTEIN S27 (METALLOPAN-STIMULIN 1) (MPS-1). [SWISSPROT;Acc:P42677] 0.228054 no value 0.221261279
2332 1.4315 TRNA ISOPENTENYLPYROPHOSPHATE TRANSFERASE. [RefSeq;Acc:NM_017646] 0.316686 TRIT1 0.221226685
2333 2.86607 SERINE/THREONINE PROTEIN PHOSPHATASE PP1-ALPHA 1 CATALYTIC SUBUNIT (EC 3.1.3.16) (PP-1A). [SWISSPROT;Acc:P08129] 0.634044 PPP1CA 0.221224185
2334 0.145754 RIBOSOME BIOGENESIS REGULATORY PROTEIN HOMOLOG. [SWISSPROT;Acc:Q15050] 0.0322443 RRS1 0.221224117
2335 0.605534 ADENOSYLHOMOCYSTEINASE (EC 3.3.1.1) (S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE) (ADOHCYASE). [SWISSPROT;Acc:P23526] 0.133936 AHCY 0.221186589
2336 0.133775 0.0295892 C1orf50 0.22118632
2337 1.15814 0.256113 D2HGDH 0.221141658
2338 0.975402 WERNER HELICASE INTERACTING PROTEIN ISOFORM 1; PUTATIVE HELICASE RUVBL; WERNER HELICASE INTERACTING PROTEIN. [RefSeq;Acc:NM_020135] 0.215454 WRNIP1 0.220887388
2339 0.303687 "6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING (EC 1.1.1.44). [SWISSPROT;Acc:P52209]" 0.0670488 PGD 0.220782582
2340 0.27731 TYPE 1 PROTEIN PHOSPHATASE INHIBITOR. [RefSeq;Acc:NM_025210] 0.0612127 PPP1R2P9 0.220737442
2341 0.968873 ARGINYL-TRNA SYNTHETASE-LIKE; ARGININE-TRNA LIGASE. [RefSeq;Acc:NM_020320] 0.21385 RARS2 0.220720363
2342 0.371844 PROTEIN PHOSPHATASE INHIBITOR 2 (IPP-2). [SWISSPROT;Acc:P41236] 0.0820717 PPP1R2 0.220715408
2343 0.490411 MEIOTIC RECOMBINATION PROTEIN DMC1/LIM15 HOMOLOG. [SWISSPROT;Acc:Q14565] 0.108234 DMC1 0.220700596
2344 0.130409 "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 TMEM91 0.220579101
2345 3.6465 "PYRUVATE DEHYDROGENASE E1 COMPONENT BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.2.4.1) (PDHE1-B). [SWISSPROT;Acc:P11177]" 0.804341 PDHB 0.220578911
2346 0.166118 THIOREDOXIN DOMAIN CONTAINING; THIOREDOXIN-RELATED TRANSMEMBRANE PROTEIN; THIOREDOXIN DOMAIN-CONTAINING. [RefSeq;Acc:NM_030755] 0.0366305 TXNDC1 0.220508915
2347 0.628094 0.1385 no value 0.220508395
2348 1.77434 TRANSCRIPTION INITIATION FACTOR TFIID 70 KDA SUBUNIT (TAFII-70) (TAFII-80) (TAFII80). [SWISSPROT;Acc:P49848] 0.391086 TAF6 0.220412097
2349 0.290417 0.0640044 PIH1D2 0.220387925
2350 0.22609 0.0498274 SLIT1 0.220387456

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/