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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Rank Gene description expected measured final Hugo
Results: HTML CSV LaTeX Showing element 2208 to 2257 of 3206 in total
Rank
description
expected
measured
final
Hugo
2208 40S RIBOSOMAL PROTEIN S3A. [SWISSPROT;Acc:P49241] 0.694888 0.156444 0.225135561 no value
2209 0.569623 0.128228 0.225110292 SLC47A1
2210 NUCLEOBINDIN 2 PRECURSOR (DNA-BINDING PROTEIN NEFA). [SWISSPROT;Acc:P80303] 0.125928 0.0283406 0.225053999 NUCB2
2211 DNA MISMATCH REPAIR PROTEIN MLH1 (MUTL PROTEIN HOMOLOG 1). [SWISSPROT;Acc:P40692] 0.972163 0.218789 0.225053823 MLH1
2212 NUCLEOBINDIN 1 PRECURSOR (CALNUC). [SWISSPROT;Acc:Q02818] 0.106724 0.0240186 0.225053409 NUCB1
2213 0.193087 0.0434449 0.225001683 LRRC48
2214 "PININ, DESMOSOME ASSOCIATED PROTEIN; PININ. [RefSeq;Acc:NM_002687]" 0.750817 0.168935 0.225001565 PNN
2215 PHOSPHOGLYCERATE KINASE 1 (EC 2.7.2.3) (PRIMER RECOGNITION PROTEIN 2) (PRP 2). [SWISSPROT;Acc:P00558] 1.2723 0.286165 0.224919437 PGK1
2216 GAMMA ENOLASE (EC 4.2.1.11) (2-PHOSPHO-D-GLYCERATE HYDRO-LYASE) (NEURAL ENOLASE) (NSE) (ENOLASE 2). [SWISSPROT;Acc:P09104] 0.22089 0.0496823 0.224918738 ENO2
2217 "PHOSPHOGLYCERATE KINASE, TESTIS SPECIFIC (EC 2.7.2.3). [SWISSPROT;Acc:P07205]" 1.17827 0.265015 0.224918737 PGK2
2218 ALPHA ENOLASE (EC 4.2.1.11) (2-PHOSPHO-D-GLYCERATE HYDRO-LYASE) (NON- NEURAL ENOLASE) (NNE) (ENOLASE 1) (PHOSPHOPYRUVATE HYDRATASE). [SWISSPROT;Acc:P06733] 0.220425 0.0495777 0.22491868 ENO1
2219 BETA ENOLASE (EC 4.2.1.11) (2-PHOSPHO-D-GLYCERATE HYDRO-LYASE) (SKELETAL MUSCLE ENOLASE) (MSE) (ENOLASE 3). [SWISSPROT;Acc:P13929] 0.24878 0.0559551 0.224918 ENO3
2220 60S RIBOSOMAL PROTEIN L21. [SWISSPROT;Acc:P46778] 0.580746 0.130589 0.224864226 no value
2221 CYTOSOLIC NONSPECIFIC DIPEPTIDASE (GLUTAMATE CARBOXYPEPTIDASE-LIKE PROTEIN 1). [SWISSPROT;Acc:Q96KP4] 1.29531 0.2912 0.224811049 CNDP2
2222 0.250658 0.0563344 0.224746068 MSRB2
2223 PHOSPHOSERINE AMINOTRANSFERASE (EC 2.6.1.52) (PSAT). [SWISSPROT;Acc:Q9Y617] 0.375987 0.0845016 PSAT1
2224 PEPTIDE METHIONINE SULFOXIDE REDUCTASE (EC 1.8.4.6) (PROTEIN- METHIONINE-S-OXIDE REDUCTASE) (PEPTIDE MET(O) REDUCTASE). [SWISSPROT;Acc:Q9UJ68] 0.125329 0.0281672 MSRA
2225 "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]" 1.36407 0.3063 0.224548594 HAO2
2226 PMS1 PROTEIN HOMOLOG 2 (DNA MISMATCH REPAIR PROTEIN PMS2). [SWISSPROT;Acc:P54278] 0.6464 0.145091 0.224460087 PMS2
2227 "ADRENODOXIN, MITOCHONDRIAL PRECURSOR (ADRENAL FERREDOXIN) (HEPATOREDOXIN) (FERREDOXIN 1). [SWISSPROT;Acc:P10109]" 1.8831 0.42248 0.22435346 FDX1
2228 XYLULOKINASE HOMOLOG; XYLULOKINASE (H. INFLUENZAE) HOMOLOG. [RefSeq;Acc:NM_005108] 1.33096 0.298587 0.224339574 XYLB
2229 AUTOPHAGY PROTEIN 12-LIKE (APG12-LIKE). [SWISSPROT;Acc:O94817] 0.876663 0.196655 0.224322231 ATG12
2230 DNA MISMATCH REPAIR PROTEIN MLH3 (MUTL PROTEIN HOMOLOG 3). [SWISSPROT;Acc:Q9UHC1] 0.522903 0.117296 0.224316938 MLH3
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] 2.72155 0.61026 0.224232515 no value
2232 APOPTOSIS-INDUCING FACTOR (AIF)-HOMOLOGOUS MITOCHONDRION-ASSOCIATED INDUCER OF DEATH; P53-RESPONSIVE GENE 3. [RefSeq;Acc:NM_032797] 1.15907 0.259882 0.224215966 AIFM2
2233 "CASEIN KINASE I, EPSILON ISOFORM (EC 2.7.1.-) (CKI-EPSILON) (CKIE). [SWISSPROT;Acc:P49674]" 1.22019 0.273568 0.224201149 no value
2234 0.251434 0.0563373 0.224063969 SPATA20
2235 "ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT ALPHA, MITOCHONDRIAL PRECURSOR (EC 1.1.1.41) (ISOCITRIC DEHYDROGENASE) (NAD+-SPECIFIC ICDH). [SWISSPROT;Acc:P50213]" 0.691419 0.154876 0.223997316 IDH3A
2236 "ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT BETA, MITOCHONDRIAL PRECURSOR (EC 1.1.1.41) (ISOCITRIC DEHYDROGENASE) (NAD+-SPECIFIC ICDH). [SWISSPROT;Acc:O43837]" 0.261755 0.0586323 0.223996867 IDH3B
2237 "ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT GAMMA, MITOCHONDRIAL PRECURSOR (EC 1.1.1.41) (ISOCITRIC DEHYDROGENASE) (NAD+-SPECIFIC ICDH). [SWISSPROT;Acc:P51553]" 0.14849299999999999 0.0332619 0.223996417 IDH3G
2238 0.988036 0.221267 0.223946293 no value
2239 "CASEIN KINASE I, DELTA ISOFORM (EC 2.7.1.-) (CKI-DELTA) (CKID). [SWISSPROT;Acc:P48730]" 1.30614 0.292497 0.223940006 CSNK1D
2240 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] 3.07116 0.687281 0.223785475 GFPT2
2241 0.130208 0.0291377 0.223778109 KIAA1033
2242 DNA-DIRECTED RNA POLYMERASE I 16 KDA POLYPEPTIDE (EC 2.7.7.6) (RPA16). [SWISSPROT;Acc:Q9Y2S0] 1.29241 0.289213 0.223778058 no value
2243 ARGININOSUCCINATE LYASE (EC 4.3.2.1) (ARGINOSUCCINASE) (ASAL). [SWISSPROT;Acc:P04424] 1.14373 0.255929 0.223766973 ASL
2244 PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE) (PBG-D). [SWISSPROT;Acc:P08397] 0.722066 0.16152 0.223691463 HMBS
2245 "ATP SYNTHASE GAMMA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P36542]" 1.26423 0.28274 0.223646014 ATP5C1
2246 "ATP SYNTHASE OLIGOMYCIN SENSITIVITY CONFERRAL PROTEIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14) (OSCP). [SWISSPROT;Acc:P48047]" ATP5O
2247 TRANSPORTIN-SR; IMPORTIN 12. [RefSeq;Acc:NM_012470] 0.289906 0.0647928 0.223495892 TNPO3
2248 CELL DIVISION CYCLE PROTEIN 23; ANAPHASE-PROMOTING COMPLEX SUBUNIT 8. [RefSeq;Acc:NM_004661] 0.418978 0.0936132 0.223432257 CDC23
2249 60S RIBOSOMAL PROTEIN L15. [SWISSPROT;Acc:P39030] 0.792735 0.176971 0.223241058 RPL15
2250 0.41666 0.0929892 0.223177651 ZCCHC7
2251 "GLYCEROL-3-PHOSPHATE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.1.99.5) (GPD-M) (GPDH-M). [SWISSPROT;Acc:P43304]" 0.50755 0.113261 0.223152399 GPD2
2252 TRANSKETOLASE-LIKE 1 (EC 2.2.1.1) (TRANSKETOLASE 2) (TK 2) (TRANSKETOLASE RELATED PROTEIN). [SWISSPROT;Acc:P51854] 0.343091 0.0765571 0.223139342 TKTL1
2253 PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY GAMMA SUBUNIT (PI3-KINASE P85-GAMMA SUBUNIT) (PTDINS-3-KINASE P85-GAMMA) (P55PIK). [SWISSPROT;Acc:Q92569] 0.267978 0.0597741 0.223055997 PIK3R3
2254 0.138615 0.0309189 0.223055946 C7orf24
2255 STEROL REGULATORY ELEMENT BINDING PROTEIN CLEAVAGE-ACTIVATING PROTEIN (SREBP CLEAVAGE-ACTIVATING PROTEIN) (SCAP). [SWISSPROT;Acc:Q12770] 0.389405 0.0868591 0.223055944 SCAP
2256 PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY ALPHA SUBUNIT (PI3-KINASE P85-ALPHA SUBUNIT) (PTDINS-3-KINASE P85-ALPHA) (PI3K). [SWISSPROT;Acc:P27986] 0.266211 0.0593799 0.223055772 PIK3R1
2257 0.389405 0.086859 0.223055688 no value

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/