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 Hugo description Rank measured final expected
Results: HTML CSV LaTeX Showing element 101 to 150 of 3206 in total
Hugo  : no value
description
Rank
measured
final
expected
"SIMILAR TO RIBOSOMAL PROTEIN, LARGE, P0. [SPTREMBL;Acc:Q96FQ9]" 1251 0.100674 0.247383617 0.406955
"SIRTUIN 7; SIR2-RELATED PROTEIN TYPE 7; SIRTUIN TYPE 7; SIRTUIN (SILENT MATING TYPE INFORMATION REGULATION 2, S.CEREVISIAE, HOMOLOG) 7; SILENT MATING TYPE INFORMATION REGULATION 2, S.CEREVISIAE, HOMOLOG 7; SIRTUIN SILENT MATING TYPE INFORMATION REGULATION" 773 0.0367538 0.263275598 0.139602
"SUCCINATE DEHYDROGENASE [UBIQUINONE] CYTOCHROME B SMALL SUBUNIT, MITOCHONDRIAL PRECURSOR (CYBS) (SUCCINATE-UBIQUINONE REDUCTASE MEMBRANE ANCHOR SUBUNIT) (QPS2) (CII-4) (SUCCINATE DEHYDROGENASE COMPLEX SUBUNIT D) (SUCCINATE-UBIQUINONE OXIDOREDUCTASE CYTOCH" 2835 0.0431276 0.193069178 0.223379
1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE ALPHA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 1) (1-AGPAT 1) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-ALPHA) (LPAAT-ALPHA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 1) (G15 PROTEIN). [SWISSPROT;Acc:Q9 2859 0.246538 0.188948413 1.30479
15 KDA SELENOPROTEIN PRECURSOR. [SWISSPROT;Acc:O60613] 698 0.0424293 0.265486775 0.159817
17 BETA-HYDROXYSTEROID DEHYDROGENASE. [SPTREMBL;Acc:Q13034] 1782 0.024834 0.23535544 0.105517
26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 12 (26S PROTEASOME REGULATORY SUBUNIT P55). [SWISSPROT;Acc:O00232] 1680 0.563839 0.238207274 2.36701
3-HYDROXYISOBUTYRYL-COENZYME A HYDROLASE. [RefSeq;Acc:NM_014362] 2566 0.512064 0.213513908 2.39827
40S RIBOSOMAL PROTEIN S15 (RIG PROTEIN). [SWISSPROT;Acc:P11174] 1943 1.32362 0.231599281 5.71513
40S RIBOSOMAL PROTEIN S18 (KE-3) (KE3). [SWISSPROT;Acc:P25232] 1998 0.543161 0.230760178 2.35379
40S RIBOSOMAL PROTEIN S2 (S4) (LLREP3 PROTEIN). [SWISSPROT;Acc:P15880] 2012 1.469 0.230625641 6.36963
40S RIBOSOMAL PROTEIN S26. [SWISSPROT;Acc:P02383] 392 0.135061 0.278606113 0.484774
40S RIBOSOMAL PROTEIN S27 (METALLOPAN-STIMULIN 1) (MPS-1). [SWISSPROT;Acc:P42677] 2331 0.228054 0.221261279 1.0307
40S RIBOSOMAL PROTEIN S28. [SWISSPROT;Acc:P25112] 1743 0.229236 0.236796681 0.968071
40S RIBOSOMAL PROTEIN S29. [SWISSPROT;Acc:P30054] 2084 0.477897 0.229020463 2.0867
40S RIBOSOMAL PROTEIN S3A. [SWISSPROT;Acc:P49241] 2208 0.156444 0.225135561 0.694888
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 0.221795621 1.84872
60S ACIDIC RIBOSOMAL PROTEIN P1. [SWISSPROT;Acc:P05386] 1322 0.310893 0.245567211 1.26602
60S RIBOSOMAL PROTEIN L10 (QM PROTEIN) (TUMOR SUPPRESSOR QM) (LAMININ RECEPTOR HOMOLOG). [SWISSPROT;Acc:P27635] 1981 1.03026 0.230989642 4.4602
60S RIBOSOMAL PROTEIN L10A (CSA-19). [SWISSPROT;Acc:P53025] 1979 0.541146 0.231023015 2.34239
60S RIBOSOMAL PROTEIN L12 LIKE PROTEIN. [SPTREMBL;Acc:O60886] 1989 0.505323 0.230916128 2.18834
60S RIBOSOMAL PROTEIN L12. [SWISSPROT;Acc:P30050] 1987 0.527851 0.230917061 2.28589
60S RIBOSOMAL PROTEIN L14 (CAG-ISL 7). [SWISSPROT;Acc:P50914] 1953 0.0571361 0.231256577 0.247068
60S RIBOSOMAL PROTEIN L17 (L23). [SWISSPROT;Acc:P18621] 1899 0.63284 0.232454948 2.72242
60S RIBOSOMAL PROTEIN L18A. [SWISSPROT;Acc:Q02543] 1844 0.214359 0.233540371 0.917867
60S RIBOSOMAL PROTEIN L21. [SWISSPROT;Acc:P46778] 2220 0.130589 0.224864226 0.580746
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 0.174142655 0.997527
60S RIBOSOMAL PROTEIN L23 (L17). [SWISSPROT;Acc:P23131] 2014 0.64348 0.230624767 2.79016
60S RIBOSOMAL PROTEIN L23A. [SWISSPROT;Acc:P29316] 1934 1.40328 0.231696263 6.05655
60S RIBOSOMAL PROTEIN L39. [SWISSPROT;Acc:P02404] 1841 0.187564 0.233540397 0.803133
60S RIBOSOMAL PROTEIN L7. [SWISSPROT;Acc:P18124] 2166 0.30758 0.227056635 1.35464
60S RIBOSOMAL PROTEIN L9. [SWISSPROT;Acc:P32969] 1814 0.788679 0.234381993 3.36493
ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1B SUBUNIT (SIGMA-ADAPTIN 1B) (ADAPTOR PROTEIN COMPLEX AP-1 SIGMA-1B SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN SIGMA-1B SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 SIGMA- 1B SMALL CHAIN) (SIGMA 1B SUBUNIT OF AP-1 CL 1161 0.127791 0.249563039 0.512059
ADAPTER-RELATED PROTEIN COMPLEX 3 BETA 2 SUBUNIT (BETA-ADAPTIN 3B) (AP-3 COMPLEX BETA-3B SUBUNIT) (BETA-3B-ADAPTIN) (NEURON-SPECIFIC VESICLE COAT PROTEIN BETA-NAP). [SWISSPROT;Acc:Q13367] 2881 0.0513128 0.184481531 0.278146
ADENINE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.7) (APRT). [SWISSPROT;Acc:P07741] 1780 0.273997 0.235356216 1.16418
ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 7 (ADP-RIBOSYLATION FACTOR-LIKE PROTEIN LAK). [SWISSPROT;Acc:P56559] 1550 0.0364961 0.241790501 0.150941
ALCOHOL DEHYDROGENASE CLASS III CHI CHAIN (EC 1.1.1.1) (GLUTATHIONE- DEPENDENT FORMALDEHYDE DEHYDROGENASE) (EC 1.2.1.1) (FDH). [SWISSPROT;Acc:P11766] 2619 0.478004 0.210499337 2.27081
ALPHA-1-ACID GLYCOPROTEIN 2 PRECURSOR (AGP 2) (OROSOMUCOID 2) (OMD 2). [SWISSPROT;Acc:P19652] 306 0.232016 0.295732065 0.784548
ALPHA-NAC PROTEIN. [SPTREMBL;Acc:Q9H009] 250 0.755644 0.311899023 2.42272
ALPHA-PARVIN (CALPONIN-LIKE INTEGRIN-LINKED KINASE BINDING PROTEIN) (CH-ILKBP). [SWISSPROT;Acc:Q9NVD7] 2507 0.0405241 0.214767765 0.188688
APOBEC-1 COMPLEMENTATION FACTOR ISOFORM 1; APOBEC-1 STIMULATING PROTEIN; APO-B RNA EDITING PROTEIN. [RefSeq;Acc:NM_014576] 261 0.0555455 0.308560398 0.180015
APOPTOSIS INHIBITOR FKSG2. [SWISSPROT;Acc:Q9HAU6] 2148 0.0544712 0.227378299 0.239562
ARSENICAL PUMP-DRIVING ATPASE (EC 3.6.3.16) (ARSENITE-TRANSLOCATING ATPASE) (ARSENICAL RESISTANCE ATPASE) (ARSENITE-TRANSPORTING ATPASE) (ARSA) (ASNA-I). [SWISSPROT;Acc:O43681] 2443 0.539817 0.217096516 2.48653
ASPARTATE BETA-HYDROXYLASE ISOFORM B; JUNCTIN ISOFORM 1; JUNCTATE; ASPARTYL/ASPARAGINYL-BETA-HYDROXYLASE; PEPTIDE-ASPARTATE BETA-DIOXYGENASE; HUMBUG. [RefSeq;Acc:NM_032468] 78 0.06383 0.406125929 0.157168
ATAXIN 2-BINDING PROTEIN. [SWISSPROT;Acc:Q9NWB1] 515 0.534301 0.272423252 1.96129
ATLASTIN; GUANYLATE-BINDING PROTEIN 3. [RefSeq;Acc:NM_015915] 3204 0.000178236 0.000219977 0.81025
BA271B5.1 (SIMILAR TO RIBOSOMAL PROTEIN S7). [SPTREMBL;Acc:Q9H1S9] 1386 0.037776 0.244468461 0.154523
BA395L14.12 (NOVEL PROTEIN SIMILAR TO SMALL NUCLEAR RIBONUCLEOPROTEIN POLYPEPTIDE A' (SNRPA1)). [SPTREMBL;Acc:Q9NU36] 313 0.482398 0.294963466 1.63545
BA508N22.1 (HSPC025) (FRAGMENT). [SPTREMBL;Acc:Q9HCW5] 745 0.0296502 0.26449777 0.1121
BASIC PROLINE-RICH PEPTIDE P-E (IB-9). [SWISSPROT;Acc:P02811] 1448 0.0700456 0.243432809 0.287741

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/