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 measured expected Hugo final
Results: HTML CSV LaTeX Showing element 2158 to 2207 of 3206 in total
Rank
description
measured
expected
Hugo
final
2158 MICROSOMAL SIGNAL PEPTIDASE 25 KDA SUBUNIT (EC 3.4.-.-) (SPASE 25 KDA SUBUNIT) (SPC25). [SWISSPROT;Acc:Q15005] 0.0254509 0.111998 SPCS2 0.227244237
2159 BACTERICIDAL PERMEABILITY-INCREASING PROTEIN PRECURSOR (BPI) (CAP 57). [SWISSPROT;Acc:P17213] 0.0196608 0.0865184 BPI 0.227244147
2160 LIPOPOLYSACCHARIDE-BINDING PROTEIN PRECURSOR (LBP). [SWISSPROT;Acc:P18428] 0.0157159 0.0691587 LBP 0.227244005
2161 URIDINE 5'-MONOPHOSPHATE SYNTHASE (UMP SYNTHASE) [INCLUDES: OROTATE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.10) (OPRTASE); OROTIDINE 5'- PHOSPHATE DECARBOXYLASE (EC 4.1.1.23) (OMPDECASE)]. [SWISSPROT;Acc:P11172] 0.485259 2.13541 UMPS 0.227243948
2162 CLEFT LIP AND PALATE ASSOCIATED TRANSMEMBRANE PROTEIN 1. [RefSeq;Acc:NM_001294] 0.0206788 0.0909983 CLPTM1 0.227243806
2163 PHOSPHOLIPID TRANSFER PROTEIN PRECURSOR (LIPID TRANSFER PROTEIN II). [SWISSPROT;Acc:P55058] 0.0139025 0.0611788 PLTP 0.227243751
2164 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 2 (26S PROTEASOME REGULATORY SUBUNIT S2) (26S PROTEASOME SUBUNIT P97) (TUMOR NECROSIS FACTOR TYPE 1 RECEPTOR ASSOCIATED PROTEIN 2) (55.11 PROTEIN). [SWISSPROT;Acc:Q13200] 0.399289 1.75758 PSMD2 0.227181124
2165 0.299286 1.31793 no value 0.227087933
2166 60S RIBOSOMAL PROTEIN L7. [SWISSPROT;Acc:P18124] 0.30758 1.35464 0.227056635
2167 SERINE PALMITOYLTRANSFERASE 1 (EC 2.3.1.50) (LONG CHAIN BASE BIOSYNTHESIS PROTEIN 1) (LCB 1) (SERINE-PALMITOYL-COA TRANSFERASE 1) (SPT 1) (SPT1). [SWISSPROT;Acc:O15269] 0.0595157 0.262124 SPTLC1 0.227051701
2168 GLYCOGENIN-2 (EC 2.4.1.186) (GN-2) (GN2). [SWISSPROT;Acc:O15488] 0.0525739 0.231578 GYG2 0.227024588
2169 GLYCOGENIN-1 (EC 2.4.1.186). [SWISSPROT;Acc:P46976] 0.0648248 0.285541 GYG1 0.22702449
2170 PROTEIN X 0001. [RefSeq;Acc:NM_016302] 0.0586994 0.25856 CRBN 0.227024288
2171 ADENOSINE KINASE (EC 2.7.1.20) (AK) (ADENOSINE 5'-PHOSPHOTRANSFERASE). [SWISSPROT;Acc:P55263] 0.156968 0.691417 ADK 0.227023634
2172 "ORNITHINE CARBAMOYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.3.3) (OTCASE) (ORNITHINE TRANSCARBAMYLASE). [SWISSPROT;Acc:P00480]" 0.235631 1.0381 OTC 0.22698295
2173 NUCLEAR PORE COMPLEX PROTEIN NUP98 (NUCLEOPORIN NUP98) (98 KDA NUCLEOPORIN). [SWISSPROT;Acc:P52948] 0.245551 1.08201 NUP98 0.226939677
2174 SCY1-LIKE 1; TELOMERASE REGULATION-ASSOCIATED PROTEIN; HT019 PROTEIN; TELOMERASE REGULATION-ASSOCIATED PROTEIN; N-TERMINAL KINASE-LIKE PROTEIN; TERATOMA-ASSOCIATED TYROSINE KINASE; N-TERMINAL KINASE-LIKE. [RefSeq;Acc:NM_020680] 0.0350787 0.154573 SCYL1 0.226939375
2175 TATA ELEMENT MODULATORY FACTOR (TMF). [SWISSPROT;Acc:P82094] TMF1
2176 MRNA-ASSOCIATED PROTEIN MRNP 41 (RAE1 PROTEIN HOMOLOG). [SWISSPROT;Acc:P78406] RAE1
2177 AMMECR1 PROTEIN. [RefSeq;Acc:NM_015365] AMMECR1
2178 ADENYLOSUCCINATE SYNTHASE-LIKE 1. [RefSeq;Acc:NM_152328] 0.385887 1.7008 ADSSL1 0.226885583
2179 ADENYLOSUCCINATE SYNTHETASE (EC 6.3.4.4) (IMP--ASPARTATE LIGASE) (ADSS) (AMPSASE). [SWISSPROT;Acc:P30520] 0.334139 1.47327 ADSS 0.226800926
2180 "GLYCINE CLEAVAGE SYSTEM H PROTEIN, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:P23434]" 0.207889 0.916816 no value 0.22675106
2181 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 6 (PAK-INTERACTING EXCHANGE FACTOR ALPHA) (ALPHA-PIX) (COOL-2). [SWISSPROT;Acc:Q15052] 0.257131 1.13453 ARHGEF6 0.226640988
2182 SERINE/THREONINE-PROTEIN KINASE PAK 2 (EC 2.7.1.-) (P21-ACTIVATED KINASE 2) (PAK-2) (PAK65) (GAMMA-PAK) (S6/H4 KINASE). [SWISSPROT;Acc:Q13177] 0.0463914 0.204773 PAK2 0.226550375
2183 SERINE/THREONINE-PROTEIN KINASE PAK 3 (EC 2.7.1.-) (P21-ACTIVATED KINASE 3) (PAK-3) (BETA-PAK) (OLIGOPHRENIN-3). [SWISSPROT;Acc:O75914] 0.048732 0.215105 PAK3 0.226549825
2184 SERINE/THREONINE-PROTEIN KINASE PAK 1 (EC 2.7.1.-) (P21-ACTIVATED KINASE 1) (PAK-1) (P65-PAK) (ALPHA-PAK). [SWISSPROT;Acc:Q13153] 0.0568471 0.250928 PAK1 0.226547456
2185 CONSERVED OLIGOMERIC GOLGI COMPLEX SUBUNIT 5 (13S GOLGI TRANSPORT COMPLEX 90 KDA SUBUNIT) (GTC-90) (GOLGI TRANSPORT COMPLEX 1). [SWISSPROT;Acc:Q9UP83] COG5
2186 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 7 (PAK-INTERACTING EXCHANGE FACTOR BETA) (BETA-PIX) (COOL-1) (P85). [SWISSPROT;Acc:Q14155] 0.214133 0.945656 ARHGEF7 0.226438578
2187 U3 SNORNP PROTEIN 4 HOMOLOG. [RefSeq;Acc:NM_033416] 0.225682 0.996773 IMP4 0.226412634
2188 0.19122 0.84475 C12orf65 0.226362829
2189 DNA-BINDING PROTEIN A (COLD SHOCK DOMAIN PROTEIN A) (SINGLE-STRAND DNA BINDING PROTEIN NF-GMB). [SWISSPROT;Acc:P16989] 0.0613805 0.271164 CSDA 0.226359325
2190 NUCLEASE SENSITIVE ELEMENT BINDING PROTEIN 1 (Y BOX BINDING PROTEIN-1) (Y-BOX TRANSCRIPTION FACTOR) (YB-1) (CCAAT-BINDING TRANSCRIPTION FACTOR I SUBUNIT A) (CBF-A) (ENHANCER FACTOR I SUBUNIT A) (EFI-A) (DNA-BINDING PROTEIN B) (DBPB). [SWISSPROT;Acc 0.0752905 0.332615 YBX1 0.226359304
2191 GERM CELL SPECIFIC Y-BOX BINDING PROTEIN; CONTRIN. [RefSeq;Acc:NM_015982] 0.0582372 0.257278 YBX2 0.226359036
2192 MEVALONATE KINASE (EC 2.7.1.36) (MK). [SWISSPROT;Acc:Q03426] 0.562681 2.48806 MVK 0.226152504
2193 DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE (EC 4.2.99.18) (AP ENDONUCLEASE 1) (APEX NUCLEASE) (APEN) (REF-1 PROTEIN). [SWISSPROT;Acc:P27695] 0.0811054 0.358823 APEX1 0.226031776
2194 "DIHYDROLIPOAMIDE ACETYLTRANSFERASE COMPONENT OF PYRUVATE DEHYDROGENASE COMPLEX, MITOCHONDRIAL PRECURSOR (EC 2.3.1.12) (E2) (PDC-E2) (70 KDA MITOCHONDRIAL AUTOANTIGEN OF PRIMARY BILIARY CIRRHOSIS) (PBC) (M2 ANTIGEN COMPLEX 70 KDA SUBUNIT). [SWISSPRO" 0.607431 2.68753 DLAT 0.226018314
2195 "AXONEMAL DYNEIN LIGHT INTERMEDIATE POLYPEPTIDE 1 (INNER DYNEIN ARM LIGHT CHAIN, AXONEMAL) (HP28). [SWISSPROT;Acc:O14645]" 0.124723 0.551845 DNALI1 0.226010927
2196 TUMOR SUPPRESSOR P53-BINDING PROTEIN 2 (P53-BINDING PROTEIN 2) (53BP2) (BCL2-BINDING PROTEIN) (BBP). [SWISSPROT;Acc:Q13625] 0.097609 0.431998 TP53BP2 0.225947805
2197 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 13B; APOPTOSIS-STIMULATING PROTEIN OF P53, 1. [RefSeq;Acc:NM_015316]" 0.0795635 0.352238 PPP1R13B 0.225879945
2198 "60S RIBOSOMAL PROTEIN L11, MITOCHONDRIAL PRECURSOR (L11MT) (CGI-113). [SWISSPROT;Acc:Q9Y3B7]" 0.568484 2.51757 MRPL11 0.225806631
2199 CYTOCHROME B5 REDUCTASE B5R.2. [RefSeq;Acc:NM_016229] 0.112427 0.497956 CYB5R2 0.225776976
2200 CYTOCHROME B5 REDUCTASE 1 (B5R.1). [RefSeq;Acc:NM_016243] 0.11223 0.497084 CYB5R1 0.22577673
2201 NADH-CYTOCHROME B5 REDUCTASE (EC 1.6.2.2) (B5R). [SWISSPROT;Acc:P00387] 0.0966308 0.427993 CYB5R3 0.22577659
2202 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 0.17129 NDST2 0.225479596
2203 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 0.14474 NDST1 0.22547948
2204 N-DEACETYLASE/N-SULFOTRANSFERASE (HEPARAN GLUCOSAMINYL) 3. [RefSeq;Acc:NM_004784] 0.0316607 0.140415 NDST3 0.225479472
2205 N-DEACETYLASE/N-SULFOTRANSFERASE 4. [RefSeq;Acc:NM_022569] 0.0319117 0.141529 NDST4 0.225478171
2206 PROTEIN CDC27HS (CELL DIVISION CYCLE PROTEIN 27 HOMOLOG) (H-NUC). [SWISSPROT;Acc:P30260] 0.244035 1.0823 CDC27 0.225478148
2207 0.098654 0.437657 SLC47A2 0.225413966

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/