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 2201 to 2250 of 3206 in total
Rank
expected
description
measured
Hugo
final
2201 0.427993 NADH-CYTOCHROME B5 REDUCTASE (EC 1.6.2.2) (B5R). [SWISSPROT;Acc:P00387] 0.0966308 CYB5R3 0.22577659
2202 0.17129 HEPARIN SULFATE N-DEACETYLASE/N-SULFOTRANSFERASE (EC 2.8.2.-) (N- HSST) (N-HEPARIN SULFATE SULFOTRANSFERASE) (GLUCOSAMINYL N- DEACETYLASE/N-SULFOTRANSFERASE). [SWISSPROT;Acc:P52849] 0.0386224 NDST2 0.225479596
2203 0.14474 HEPARAN SULFATE N-DEACETYLASE/N-SULFOTRANSFERASE (EC 2.8.2.8) (N-HSST) (HSNST) ([HEPARAN SULFATE]-GLUCOSAMINE N-SULFOTRANSFERASE) (N-HEPARAN SULFATE SULFOTRANSFERASE) (GLUCOSAMINYL N-DEACETYLASE/N- SULFOTRANSFERASE). [SWISSPROT;Acc:P52848] 0.0326359 NDST1 0.22547948
2204 0.140415 N-DEACETYLASE/N-SULFOTRANSFERASE (HEPARAN GLUCOSAMINYL) 3. [RefSeq;Acc:NM_004784] 0.0316607 NDST3 0.225479472
2205 0.141529 N-DEACETYLASE/N-SULFOTRANSFERASE 4. [RefSeq;Acc:NM_022569] 0.0319117 NDST4 0.225478171
2206 1.0823 PROTEIN CDC27HS (CELL DIVISION CYCLE PROTEIN 27 HOMOLOG) (H-NUC). [SWISSPROT;Acc:P30260] 0.244035 CDC27 0.225478148
2207 0.437657 0.098654 SLC47A2 0.225413966
2208 0.694888 40S RIBOSOMAL PROTEIN S3A. [SWISSPROT;Acc:P49241] 0.156444 no value 0.225135561
2209 0.569623 0.128228 SLC47A1 0.225110292
2210 0.125928 NUCLEOBINDIN 2 PRECURSOR (DNA-BINDING PROTEIN NEFA). [SWISSPROT;Acc:P80303] 0.0283406 NUCB2 0.225053999
2211 0.972163 DNA MISMATCH REPAIR PROTEIN MLH1 (MUTL PROTEIN HOMOLOG 1). [SWISSPROT;Acc:P40692] 0.218789 MLH1 0.225053823
2212 0.106724 NUCLEOBINDIN 1 PRECURSOR (CALNUC). [SWISSPROT;Acc:Q02818] 0.0240186 NUCB1 0.225053409
2213 0.193087 0.0434449 LRRC48 0.225001683
2214 0.750817 "PININ, DESMOSOME ASSOCIATED PROTEIN; PININ. [RefSeq;Acc:NM_002687]" 0.168935 PNN 0.225001565
2215 1.2723 PHOSPHOGLYCERATE KINASE 1 (EC 2.7.2.3) (PRIMER RECOGNITION PROTEIN 2) (PRP 2). [SWISSPROT;Acc:P00558] 0.286165 PGK1 0.224919437
2216 0.22089 GAMMA ENOLASE (EC 4.2.1.11) (2-PHOSPHO-D-GLYCERATE HYDRO-LYASE) (NEURAL ENOLASE) (NSE) (ENOLASE 2). [SWISSPROT;Acc:P09104] 0.0496823 ENO2 0.224918738
2217 1.17827 "PHOSPHOGLYCERATE KINASE, TESTIS SPECIFIC (EC 2.7.2.3). [SWISSPROT;Acc:P07205]" 0.265015 PGK2 0.224918737
2218 0.220425 ALPHA ENOLASE (EC 4.2.1.11) (2-PHOSPHO-D-GLYCERATE HYDRO-LYASE) (NON- NEURAL ENOLASE) (NNE) (ENOLASE 1) (PHOSPHOPYRUVATE HYDRATASE). [SWISSPROT;Acc:P06733] 0.0495777 ENO1 0.22491868
2219 0.24878 BETA ENOLASE (EC 4.2.1.11) (2-PHOSPHO-D-GLYCERATE HYDRO-LYASE) (SKELETAL MUSCLE ENOLASE) (MSE) (ENOLASE 3). [SWISSPROT;Acc:P13929] 0.0559551 ENO3 0.224918
2220 0.580746 60S RIBOSOMAL PROTEIN L21. [SWISSPROT;Acc:P46778] 0.130589 no value 0.224864226
2221 1.29531 CYTOSOLIC NONSPECIFIC DIPEPTIDASE (GLUTAMATE CARBOXYPEPTIDASE-LIKE PROTEIN 1). [SWISSPROT;Acc:Q96KP4] 0.2912 CNDP2 0.224811049
2222 0.250658 0.0563344 MSRB2 0.224746068
2223 0.375987 PHOSPHOSERINE AMINOTRANSFERASE (EC 2.6.1.52) (PSAT). [SWISSPROT;Acc:Q9Y617] 0.0845016 PSAT1
2224 0.125329 PEPTIDE METHIONINE SULFOXIDE REDUCTASE (EC 1.8.4.6) (PROTEIN- METHIONINE-S-OXIDE REDUCTASE) (PEPTIDE MET(O) REDUCTASE). [SWISSPROT;Acc:Q9UJ68] 0.0281672 MSRA
2225 1.36407 "HYDROXYACID OXIDASE 2 (EC 1.1.3.15) (HAOX2) ((S)-2-HYDROXY-ACID OXIDASE, PEROXISOMAL) (LONG CHAIN ALPHA-HYDROXY ACID OXIDASE) (LONG- CHAIN L-2-HYDROXY ACID OXIDASE). [SWISSPROT;Acc:Q9NYQ3]" 0.3063 HAO2 0.224548594
2226 0.6464 PMS1 PROTEIN HOMOLOG 2 (DNA MISMATCH REPAIR PROTEIN PMS2). [SWISSPROT;Acc:P54278] 0.145091 PMS2 0.224460087
2227 1.8831 "ADRENODOXIN, MITOCHONDRIAL PRECURSOR (ADRENAL FERREDOXIN) (HEPATOREDOXIN) (FERREDOXIN 1). [SWISSPROT;Acc:P10109]" 0.42248 FDX1 0.22435346
2228 1.33096 XYLULOKINASE HOMOLOG; XYLULOKINASE (H. INFLUENZAE) HOMOLOG. [RefSeq;Acc:NM_005108] 0.298587 XYLB 0.224339574
2229 0.876663 AUTOPHAGY PROTEIN 12-LIKE (APG12-LIKE). [SWISSPROT;Acc:O94817] 0.196655 ATG12 0.224322231
2230 0.522903 DNA MISMATCH REPAIR PROTEIN MLH3 (MUTL PROTEIN HOMOLOG 3). [SWISSPROT;Acc:Q9UHC1] 0.117296 MLH3 0.224316938
2231 2.72155 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] 0.61026 no value 0.224232515
2232 1.15907 APOPTOSIS-INDUCING FACTOR (AIF)-HOMOLOGOUS MITOCHONDRION-ASSOCIATED INDUCER OF DEATH; P53-RESPONSIVE GENE 3. [RefSeq;Acc:NM_032797] 0.259882 AIFM2 0.224215966
2233 1.22019 "CASEIN KINASE I, EPSILON ISOFORM (EC 2.7.1.-) (CKI-EPSILON) (CKIE). [SWISSPROT;Acc:P49674]" 0.273568 no value 0.224201149
2234 0.251434 0.0563373 SPATA20 0.224063969
2235 0.691419 "ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT ALPHA, MITOCHONDRIAL PRECURSOR (EC 1.1.1.41) (ISOCITRIC DEHYDROGENASE) (NAD+-SPECIFIC ICDH). [SWISSPROT;Acc:P50213]" 0.154876 IDH3A 0.223997316
2236 0.261755 "ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT BETA, MITOCHONDRIAL PRECURSOR (EC 1.1.1.41) (ISOCITRIC DEHYDROGENASE) (NAD+-SPECIFIC ICDH). [SWISSPROT;Acc:O43837]" 0.0586323 IDH3B 0.223996867
2237 0.14849299999999999 "ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT GAMMA, MITOCHONDRIAL PRECURSOR (EC 1.1.1.41) (ISOCITRIC DEHYDROGENASE) (NAD+-SPECIFIC ICDH). [SWISSPROT;Acc:P51553]" 0.0332619 IDH3G 0.223996417
2238 0.988036 0.221267 no value 0.223946293
2239 1.30614 "CASEIN KINASE I, DELTA ISOFORM (EC 2.7.1.-) (CKI-DELTA) (CKID). [SWISSPROT;Acc:P48730]" 0.292497 CSNK1D 0.223940006
2240 3.07116 GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 2 (EC 2.6.1.16) (HEXOSEPHOSPHATE AMINOTRANSFERASE 2) (D-FRUCTOSE-6- PHOSPHATE AMIDOTRANSFERASE 2) (GFAT 2) (GFAT2). [SWISSPROT;Acc:O94808] 0.687281 GFPT2 0.223785475
2241 0.130208 0.0291377 KIAA1033 0.223778109
2242 1.29241 DNA-DIRECTED RNA POLYMERASE I 16 KDA POLYPEPTIDE (EC 2.7.7.6) (RPA16). [SWISSPROT;Acc:Q9Y2S0] 0.289213 no value 0.223778058
2243 1.14373 ARGININOSUCCINATE LYASE (EC 4.3.2.1) (ARGINOSUCCINASE) (ASAL). [SWISSPROT;Acc:P04424] 0.255929 ASL 0.223766973
2244 0.722066 PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE) (PBG-D). [SWISSPROT;Acc:P08397] 0.16152 HMBS 0.223691463
2245 1.26423 "ATP SYNTHASE GAMMA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P36542]" 0.28274 ATP5C1 0.223646014
2246 "ATP SYNTHASE OLIGOMYCIN SENSITIVITY CONFERRAL PROTEIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14) (OSCP). [SWISSPROT;Acc:P48047]" ATP5O
2247 0.289906 TRANSPORTIN-SR; IMPORTIN 12. [RefSeq;Acc:NM_012470] 0.0647928 TNPO3 0.223495892
2248 0.418978 CELL DIVISION CYCLE PROTEIN 23; ANAPHASE-PROMOTING COMPLEX SUBUNIT 8. [RefSeq;Acc:NM_004661] 0.0936132 CDC23 0.223432257
2249 0.792735 60S RIBOSOMAL PROTEIN L15. [SWISSPROT;Acc:P39030] 0.176971 RPL15 0.223241058
2250 0.41666 0.0929892 ZCCHC7 0.223177651

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/