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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description Rank Gene measured expected final Hugo
Results: HTML CSV LaTeX Showing element 951 to 1000 of 3206 in total
description
Rank
measured
expected
final
Hugo
40S RIBOSOMAL PROTEIN S16. [SWISSPROT;Acc:P17008] 2018 0.590899 2.56327 0.230525462 RPS16
40S RIBOSOMAL PROTEIN S18 (KE-3) (KE3). [SWISSPROT;Acc:P25232] 1998 0.543161 2.35379 0.230760178 no value
40S RIBOSOMAL PROTEIN S19. [SWISSPROT;Acc:P39019] 1843 0.187564 0.803133 0.233540397 RPS19
40S RIBOSOMAL PROTEIN S2 (S4) (LLREP3 PROTEIN). [SWISSPROT;Acc:P15880] 2012 1.469 6.36963 0.230625641 no value
40S RIBOSOMAL PROTEIN S20. [SWISSPROT;Acc:P17075] 2005 0.834926 3.6186 0.230731775 RPS20
40S RIBOSOMAL PROTEIN S21. [SWISSPROT;Acc:P35265] 2323 0.187278 0.844371 0.221795869 RPS21
40S RIBOSOMAL PROTEIN S23. [SWISSPROT;Acc:P39028] 1986 0.485913 2.1041 0.230936267 RPS23
40S RIBOSOMAL PROTEIN S24 (S19). [SWISSPROT;Acc:P16632] 1839 0.182207 0.780167 0.233548715 RPS24
40S RIBOSOMAL PROTEIN S26. [SWISSPROT;Acc:P02383] 392 0.135061 0.484774 0.278606113 no value
40S RIBOSOMAL PROTEIN S27 (METALLOPAN-STIMULIN 1) (MPS-1). [SWISSPROT;Acc:P42677] 2331 0.228054 1.0307 0.221261279
40S RIBOSOMAL PROTEIN S28. [SWISSPROT;Acc:P25112] 1743 0.229236 0.968071 0.236796681
40S RIBOSOMAL PROTEIN S29. [SWISSPROT;Acc:P30054] 2084 0.477897 2.0867 0.229020463
40S RIBOSOMAL PROTEIN S3. [SWISSPROT;Acc:P23396] 1908 1.51643 6.5312 0.232182447 RPS3
40S RIBOSOMAL PROTEIN S30. [SWISSPROT;Acc:Q05472] 864 0.124733 0.479216 0.26028555 FAU
40S RIBOSOMAL PROTEIN S3A. [SWISSPROT;Acc:P49241] 2208 0.156444 0.694888 0.225135561 no value
40S RIBOSOMAL PROTEIN S5. [SWISSPROT;Acc:P46782] 2036 1.08774 4.7257 0.230175424 RPS5
40S RIBOSOMAL PROTEIN S7 (S8). [SWISSPROT;Acc:P23821] 1388 0.038293 0.156638 0.244468137 RPS7
40S RIBOSOMAL PROTEIN S8. [SWISSPROT;Acc:P09058] 588 0.122515 0.454799 0.269382738 RPS8
40S RIBOSOMAL PROTEIN S9. [SWISSPROT;Acc:P46781] 1970 0.305347 1.32095 0.231157122 RPS9
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] 2325 0.410038 1.84872 0.221795621 no value
43 KDA RECEPTOR-ASSOCIATED PROTEIN OF THE SYNAPSE (RAPSYN) (ACETYLCHOLINE RECEPTOR-ASSOCIATED 43 KDA PROTEIN) (43 KDA POSTSYNAPTIC PROTEIN). [SWISSPROT;Acc:Q13702] 758 0.552551 2.09375 0.263904955 RAPSN
44050 PROTEIN. [RefSeq;Acc:NM_178832] 1666 0.03729 0.156155 0.238801191 C10orf83
45 KDA CALCIUM-BINDING PROTEIN PRECURSOR (CAB45) (STROMAL CELL-DERIVED FACTOR 4) (SDF-4). [SWISSPROT;Acc:Q9BRK5] 2468 0.0737619 0.340556 0.216592572 SDF4
5'-METHYLTHIOADENOSINE PHOSPHORYLASE (EC 2.4.2.28) (MTA PHOSPHORYLASE) (MTAPASE). [SWISSPROT;Acc:Q13126] 590 0.12174 0.452001 0.269335687 MTAP
6-PHOSPHOGLUCONOLACTONASE (EC 3.1.1.31) (6PGL). [SWISSPROT;Acc:O95336] 2449 0.0750119 0.345603 0.217046438 PGLS
60 KDA TAT INTERACTIVE PROTEIN (TIP60) (HIV-1 TAT INTERACTIVE PROTEIN) (CPLA(2) INTERACTING PROTEIN). [SWISSPROT;Acc:Q92993] 981 0.0395897 0.155084 0.255279075 HTATIP
60S ACIDIC RIBOSOMAL PROTEIN P0 (L10E). [SWISSPROT;Acc:P05388] 1249 0.11779 0.476127 0.247391977 RPLP0
60S ACIDIC RIBOSOMAL PROTEIN P1. [SWISSPROT;Acc:P05386] 1322 0.310893 1.26602 0.245567211 no value
60S ACIDIC RIBOSOMAL PROTEIN P2. [SWISSPROT;Acc:P05387] 976 0.114475 0.44823 0.255393436 RPLP2
60S RIBOSOMAL PROTEIN L10 (QM PROTEIN) (TUMOR SUPPRESSOR QM) (LAMININ RECEPTOR HOMOLOG). [SWISSPROT;Acc:P27635] 1981 1.03026 4.4602 0.230989642 no value
60S RIBOSOMAL PROTEIN L10A (CSA-19). [SWISSPROT;Acc:P53025] 1979 0.541146 2.34239 0.231023015
60S RIBOSOMAL PROTEIN L11. [SWISSPROT;Acc:P39026] 2058 0.609415 2.65323 0.229687965 RPL11
60S RIBOSOMAL PROTEIN L12 LIKE PROTEIN. [SPTREMBL;Acc:O60886] 1989 0.505323 2.18834 0.230916128 no value
60S RIBOSOMAL PROTEIN L12. [SWISSPROT;Acc:P30050] 1987 0.527851 2.28589 0.230917061
60S RIBOSOMAL PROTEIN L13A (23 KDA HIGHLY BASIC PROTEIN). [SWISSPROT;Acc:P40429] 2020 0.587935 2.55045 0.230522065 RPL13A
60S RIBOSOMAL PROTEIN L14 (CAG-ISL 7). [SWISSPROT;Acc:P50914] 1953 0.0571361 0.247068 0.231256577 no value
60S RIBOSOMAL PROTEIN L15. [SWISSPROT;Acc:P39030] 2249 0.176971 0.792735 0.223241058 RPL15
60S RIBOSOMAL PROTEIN L17 (L23). [SWISSPROT;Acc:P18621] 1899 0.63284 2.72242 0.232454948 no value
60S RIBOSOMAL PROTEIN L18. [SWISSPROT;Acc:Q07020] 2132 0.35482 1.55638 0.227977743 RPL18
60S RIBOSOMAL PROTEIN L18A. [SWISSPROT;Acc:Q02543] 1844 0.214359 0.917867 0.233540371 no value
60S RIBOSOMAL PROTEIN L19. [SWISSPROT;Acc:P14118] 1290 0.864722 3.51639 0.245911858 RPL19
60S RIBOSOMAL PROTEIN L21. [SWISSPROT;Acc:P46778] 2220 0.130589 0.580746 0.224864226 no value
60S RIBOSOMAL PROTEIN L22 (EPSTEIN-BARR VIRUS SMALL RNA ASSOCIATED PROTEIN) (EBER ASSOCIATED PROTEIN) (EAP) (HEPARIN BINDING PROTEIN HBP15). [SWISSPROT;Acc:P35268] 2903 0.173712 0.997527 0.174142655
60S RIBOSOMAL PROTEIN L23 (L17). [SWISSPROT;Acc:P23131] 2014 0.64348 2.79016 0.230624767
60S RIBOSOMAL PROTEIN L23A. [SWISSPROT;Acc:P29316] 1934 1.40328 6.05655 0.231696263
60S RIBOSOMAL PROTEIN L24 (L30). [SWISSPROT;Acc:P38663] 956 0.308685 1.20423 0.256333923 RPL24
60S RIBOSOMAL PROTEIN L26. [SWISSPROT;Acc:Q02877] 1945 1.32337 5.71481 0.231568504 RPL26
60S RIBOSOMAL PROTEIN L28. [SWISSPROT;Acc:P46779] 1604 0.0701119 0.292225 0.239924373 RPL28
60S RIBOSOMAL PROTEIN L29 (CELL SURFACE HEPARIN BINDING PROTEIN HIP). [SWISSPROT;Acc:P47914] 2383 0.0507615 0.231055 0.219694445 RPL29
60S RIBOSOMAL PROTEIN L3-LIKE. [SWISSPROT;Acc:Q92901] 1893 1.34083 5.76236 0.232687649 RPL3L

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/