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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Hugo measured Gene expected Rank description final
Results: HTML CSV LaTeX Showing element 302 to 351 of 3206 in total
Hugo
measured
expected
Rank
description
final
no value 0.448528 1.82552 1316 TGF BETA-INDUCIBLE NUCLEAR PROTEIN 1; HAIRY CELL LEUKEMIA PROTEIN 1. [RefSeq;Acc:NM_014886] 0.24569876
0.477897 2.0867 2084 40S RIBOSOMAL PROTEIN S29. [SWISSPROT;Acc:P30054] 0.229020463
0.478004 2.27081 2619 ALCOHOL DEHYDROGENASE CLASS III CHI CHAIN (EC 1.1.1.1) (GLUTATHIONE- DEPENDENT FORMALDEHYDE DEHYDROGENASE) (EC 1.2.1.1) (FDH). [SWISSPROT;Acc:P11766] 0.210499337
0.481793 1.95026 1264 LAMIN B2. [SWISSPROT;Acc:Q03252] 0.247040395
0.482398 1.63545 313 BA395L14.12 (NOVEL PROTEIN SIMILAR TO SMALL NUCLEAR RIBONUCLEOPROTEIN POLYPEPTIDE A' (SNRPA1)). [SPTREMBL;Acc:Q9NU36] 0.294963466
0.492676 1.87133 772 CASEIN KINASE II BETA CHAIN (CK II) (PHOSVITIN) (G5A). [SWISSPROT;Acc:P13862] 0.263275852
0.505323 2.18834 1989 60S RIBOSOMAL PROTEIN L12 LIKE PROTEIN. [SPTREMBL;Acc:O60886] 0.230916128
0.512064 2.39827 2566 3-HYDROXYISOBUTYRYL-COENZYME A HYDROLASE. [RefSeq;Acc:NM_014362] 0.213513908
0.512921 2.22124 1988 DJ999L4.1 (NOVEL PROTEIN SIMILAR TO RIBOSOMAL PROTEIN L12 (RPL12)). [SPTREMBL;Acc:Q9NQ02] 0.230916515
0.52666 1.98825 712 HISTONE DEACETYLASE 2 (HD2). [SWISSPROT;Acc:Q92769] 0.264886206
0.527851 2.28589 1987 60S RIBOSOMAL PROTEIN L12. [SWISSPROT;Acc:P30050] 0.230917061
0.533964 2.31472 2009 NUCLEOSIDE DIPHOSPHATE KINASE B (EC 2.7.4.6) (NDK B) (NDP KINASE B) (NM23-H2) (C-MYC PURINE-BINDING TRANSCRIPTION FACTOR PUF). [SWISSPROT;Acc:P22392] 0.230681897
0.534301 1.96129 515 ATAXIN 2-BINDING PROTEIN. [SWISSPROT;Acc:Q9NWB1] 0.272423252
0.539175 1.99055 560 ELAV-LIKE PROTEIN 3 (HU-ANTIGEN C) (HUC) (PARANEOPLASTIC CEREBELLAR DEGENERATION-ASSOCIATED ANTIGEN) (PARANEOPLASTIC LIMBIC ENCEPHALITIS ANTIGEN 21). [SWISSPROT;Acc:Q14576] 0.270867348
0.539817 2.48653 2443 ARSENICAL PUMP-DRIVING ATPASE (EC 3.6.3.16) (ARSENITE-TRANSLOCATING ATPASE) (ARSENICAL RESISTANCE ATPASE) (ARSENITE-TRANSPORTING ATPASE) (ARSA) (ASNA-I). [SWISSPROT;Acc:O43681] 0.217096516
0.541146 2.34239 1979 60S RIBOSOMAL PROTEIN L10A (CSA-19). [SWISSPROT;Acc:P53025] 0.231023015
0.542979 2.61855 2707 0.207358653
0.543161 2.35379 1998 40S RIBOSOMAL PROTEIN S18 (KE-3) (KE3). [SWISSPROT;Acc:P25232] 0.230760178
0.549308 2.36366 1902 0.232397214
0.563143 2.05361 499 SEVEN IN ABSENTIA HOMOLOG 1. [RefSeq;Acc:NM_003031] 0.274221006
0.563839 2.36701 1680 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 12 (26S PROTEASOME REGULATORY SUBUNIT P55). [SWISSPROT;Acc:O00232] 0.238207274
0.572386 2.31408 1253 IMPORTIN 4. [RefSeq;Acc:NM_024658] 0.247349271
0.596229 2.43411 1362 0.244947435
0.61026 2.72155 2231 GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 1 (EC 2.6.1.16) (HEXOSEPHOSPHATE AMINOTRANSFERASE 1) (D-FRUCTOSE-6- PHOSPHATE AMIDOTRANSFERASE 1) (GFAT 1) (GFAT1). [SWISSPROT;Acc:Q06210] 0.224232515
0.625831 2.00343 247 TRANSCRIPTION FACTOR BTF3 HOMOLOG 3. [SWISSPROT;Acc:Q13892] 0.312379769
0.63284 2.72242 1899 60S RIBOSOMAL PROTEIN L17 (L23). [SWISSPROT;Acc:P18621] 0.232454948
0.64348 2.79016 2014 60S RIBOSOMAL PROTEIN L23 (L17). [SWISSPROT;Acc:P23131] 0.230624767
0.676836 2.7231 1194 PROTEASOME SUBUNIT BETA TYPE 8 PRECURSOR (EC 3.4.25.1) (PROTEASOME COMPONENT C13) (MACROPAIN SUBUNIT C13) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C13). [SWISSPROT;Acc:P28062] 0.248553487
0.694134 2.5522 522 "PRE-MRNA CLEAVAGE FACTOR I, 59 KDA SUBUNIT. [RefSeq;Acc:NM_024811]" 0.271974767
0.704795 3.04081 1928 0.231778704
0.707942 3.07604 2040 "40S RIBOSOMAL PROTEIN S4, X ISOFORM (SINGLE COPY ABUNDANT MRNA PROTEIN) (SCR10). [SWISSPROT;Acc:P12750]" 0.230147202
0.743299 2.38318 251 0.311893772
0.745512 3.26763 2119 "PEROXISOMAL 3,2-TRANS-ENOYL-COA ISOMERASE (EC 5.3.3.8) (DODECENOYL-COA DELTA-ISOMERASE) (D3,D2-ENOYL-COA ISOMERASE) (DBI-RELATED PROTEIN 1) (DRS-1) (HEPATOCELLULAR CARCINOMA-ASSOCIATED ANTIGEN 88). [SWISSPROT;Acc:O75521]" 0.228150678
0.755644 2.42272 250 ALPHA-NAC PROTEIN. [SPTREMBL;Acc:Q9H009] 0.311899023
0.788679 3.36493 1814 60S RIBOSOMAL PROTEIN L9. [SWISSPROT;Acc:P32969] 0.234381993
0.788778 2.02915 85 TRANSCRIPTION FACTOR DP-1 (E2F DIMERIZATION PARTNER 1) (DRTF1- POLYPEPTIDE-1) (DRTF1). [SWISSPROT;Acc:Q14186] 0.388723357
0.804734 2.57998 249 NASCENT-POLYPEPTIDE-ASSOCIATED COMPLEX ALPHA POLYPEPTIDE. [RefSeq;Acc:NM_005594] 0.311914821
0.839834 4.39067 2852 SMALL GLUTAMINE RICH PROTEIN WITH TETRATRICOPEPTIDE REPEATS 2. [RefSeq;Acc:NM_019072] 0.191276958
0.914796 2.37847 92 0.38461532
1.02862 4.7857 2502 KERATIN ASSOCIATED PROTEIN 9-4; KERATIN ASSOCIATED PROTEIN 9.4. [RefSeq;Acc:NM_033191] 0.214936164
1.03026 4.4602 1981 60S RIBOSOMAL PROTEIN L10 (QM PROTEIN) (TUMOR SUPPRESSOR QM) (LAMININ RECEPTOR HOMOLOG). [SWISSPROT;Acc:P27635] 0.230989642
1.04135 4.48455 1906 SUPPRESSOR OF TY 5 HOMOLOG; SUPPRESSOR OF TY (S.CEREVISIAE) 5 HOMOLOG. [RefSeq;Acc:NM_003169] 0.23220836
1.08194 3.53138 269 SPLICING FACTOR 3B SUBUNIT 3 (SPLICEOSOME ASSOCIATED PROTEIN 130) (SAP 130) (SF3B130) (PRE-MRNA SPLICING FACTOR SF3B 130 KDA SUBUNIT). [SWISSPROT;Acc:Q15393] 0.306378809
1.24769 5.38515 1935 C367G8.3 (NOVEL PROTEIN SIMILAR TO RPL23A (60S RIBOSOMAL PROTEIN L23A)) (60S RIBOSOMAL PROTEIN L23A LIKE). [SPTREMBL;Acc:Q9BR02] 0.231690854
1.27676 5.53686 2016 PUTATIVE EUKARYOTIC TRANSLATION INITIATION FACTOR 1A (EIF-1A) (EIF- 4C). [SWISSPROT;Acc:O75642] 0.230592791
1.32362 5.71513 1943 40S RIBOSOMAL PROTEIN S15 (RIG PROTEIN). [SWISSPROT;Acc:P11174] 0.231599281
1.40328 6.05655 1934 60S RIBOSOMAL PROTEIN L23A. [SWISSPROT;Acc:P29316] 0.231696263
1.469 6.36963 2012 40S RIBOSOMAL PROTEIN S2 (S4) (LLREP3 PROTEIN). [SWISSPROT;Acc:P15880] 0.230625641
3.66001 3.3348 4 1.097520091
AAK1 0.168547 0.60766 423 ADAPTOR-ASSOCIATED KINASE 1. [RefSeq;Acc:NM_014911] 0.277370569

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/