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 measured Gene description Hugo expected final
Results: HTML CSV LaTeX Showing element 2158 to 2207 of 3206 in total
Rank
measured
description
Hugo
expected
final
2158 0.0254509 MICROSOMAL SIGNAL PEPTIDASE 25 KDA SUBUNIT (EC 3.4.-.-) (SPASE 25 KDA SUBUNIT) (SPC25). [SWISSPROT;Acc:Q15005] SPCS2 0.111998 0.227244237
2159 0.0196608 BACTERICIDAL PERMEABILITY-INCREASING PROTEIN PRECURSOR (BPI) (CAP 57). [SWISSPROT;Acc:P17213] BPI 0.0865184 0.227244147
2160 0.0157159 LIPOPOLYSACCHARIDE-BINDING PROTEIN PRECURSOR (LBP). [SWISSPROT;Acc:P18428] LBP 0.0691587 0.227244005
2161 0.485259 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] UMPS 2.13541 0.227243948
2162 0.0206788 CLEFT LIP AND PALATE ASSOCIATED TRANSMEMBRANE PROTEIN 1. [RefSeq;Acc:NM_001294] CLPTM1 0.0909983 0.227243806
2163 0.0139025 PHOSPHOLIPID TRANSFER PROTEIN PRECURSOR (LIPID TRANSFER PROTEIN II). [SWISSPROT;Acc:P55058] PLTP 0.0611788 0.227243751
2164 0.399289 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] PSMD2 1.75758 0.227181124
2165 0.299286 no value 1.31793 0.227087933
2166 0.30758 60S RIBOSOMAL PROTEIN L7. [SWISSPROT;Acc:P18124] 1.35464 0.227056635
2167 0.0595157 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] SPTLC1 0.262124 0.227051701
2168 0.0525739 GLYCOGENIN-2 (EC 2.4.1.186) (GN-2) (GN2). [SWISSPROT;Acc:O15488] GYG2 0.231578 0.227024588
2169 0.0648248 GLYCOGENIN-1 (EC 2.4.1.186). [SWISSPROT;Acc:P46976] GYG1 0.285541 0.22702449
2170 0.0586994 PROTEIN X 0001. [RefSeq;Acc:NM_016302] CRBN 0.25856 0.227024288
2171 0.156968 ADENOSINE KINASE (EC 2.7.1.20) (AK) (ADENOSINE 5'-PHOSPHOTRANSFERASE). [SWISSPROT;Acc:P55263] ADK 0.691417 0.227023634
2172 0.235631 "ORNITHINE CARBAMOYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.3.3) (OTCASE) (ORNITHINE TRANSCARBAMYLASE). [SWISSPROT;Acc:P00480]" OTC 1.0381 0.22698295
2173 0.245551 NUCLEAR PORE COMPLEX PROTEIN NUP98 (NUCLEOPORIN NUP98) (98 KDA NUCLEOPORIN). [SWISSPROT;Acc:P52948] NUP98 1.08201 0.226939677
2174 0.0350787 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] SCYL1 0.154573 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 0.385887 ADENYLOSUCCINATE SYNTHASE-LIKE 1. [RefSeq;Acc:NM_152328] ADSSL1 1.7008 0.226885583
2179 0.334139 ADENYLOSUCCINATE SYNTHETASE (EC 6.3.4.4) (IMP--ASPARTATE LIGASE) (ADSS) (AMPSASE). [SWISSPROT;Acc:P30520] ADSS 1.47327 0.226800926
2180 0.207889 "GLYCINE CLEAVAGE SYSTEM H PROTEIN, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:P23434]" no value 0.916816 0.22675106
2181 0.257131 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 6 (PAK-INTERACTING EXCHANGE FACTOR ALPHA) (ALPHA-PIX) (COOL-2). [SWISSPROT;Acc:Q15052] ARHGEF6 1.13453 0.226640988
2182 0.0463914 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] PAK2 0.204773 0.226550375
2183 0.048732 SERINE/THREONINE-PROTEIN KINASE PAK 3 (EC 2.7.1.-) (P21-ACTIVATED KINASE 3) (PAK-3) (BETA-PAK) (OLIGOPHRENIN-3). [SWISSPROT;Acc:O75914] PAK3 0.215105 0.226549825
2184 0.0568471 SERINE/THREONINE-PROTEIN KINASE PAK 1 (EC 2.7.1.-) (P21-ACTIVATED KINASE 1) (PAK-1) (P65-PAK) (ALPHA-PAK). [SWISSPROT;Acc:Q13153] PAK1 0.250928 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 0.214133 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 7 (PAK-INTERACTING EXCHANGE FACTOR BETA) (BETA-PIX) (COOL-1) (P85). [SWISSPROT;Acc:Q14155] ARHGEF7 0.945656 0.226438578
2187 0.225682 U3 SNORNP PROTEIN 4 HOMOLOG. [RefSeq;Acc:NM_033416] IMP4 0.996773 0.226412634
2188 0.19122 C12orf65 0.84475 0.226362829
2189 0.0613805 DNA-BINDING PROTEIN A (COLD SHOCK DOMAIN PROTEIN A) (SINGLE-STRAND DNA BINDING PROTEIN NF-GMB). [SWISSPROT;Acc:P16989] CSDA 0.271164 0.226359325
2190 0.0752905 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 YBX1 0.332615 0.226359304
2191 0.0582372 GERM CELL SPECIFIC Y-BOX BINDING PROTEIN; CONTRIN. [RefSeq;Acc:NM_015982] YBX2 0.257278 0.226359036
2192 0.562681 MEVALONATE KINASE (EC 2.7.1.36) (MK). [SWISSPROT;Acc:Q03426] MVK 2.48806 0.226152504
2193 0.0811054 DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE (EC 4.2.99.18) (AP ENDONUCLEASE 1) (APEX NUCLEASE) (APEN) (REF-1 PROTEIN). [SWISSPROT;Acc:P27695] APEX1 0.358823 0.226031776
2194 0.607431 "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" DLAT 2.68753 0.226018314
2195 0.124723 "AXONEMAL DYNEIN LIGHT INTERMEDIATE POLYPEPTIDE 1 (INNER DYNEIN ARM LIGHT CHAIN, AXONEMAL) (HP28). [SWISSPROT;Acc:O14645]" DNALI1 0.551845 0.226010927
2196 0.097609 TUMOR SUPPRESSOR P53-BINDING PROTEIN 2 (P53-BINDING PROTEIN 2) (53BP2) (BCL2-BINDING PROTEIN) (BBP). [SWISSPROT;Acc:Q13625] TP53BP2 0.431998 0.225947805
2197 0.0795635 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 13B; APOPTOSIS-STIMULATING PROTEIN OF P53, 1. [RefSeq;Acc:NM_015316]" PPP1R13B 0.352238 0.225879945
2198 0.568484 "60S RIBOSOMAL PROTEIN L11, MITOCHONDRIAL PRECURSOR (L11MT) (CGI-113). [SWISSPROT;Acc:Q9Y3B7]" MRPL11 2.51757 0.225806631
2199 0.112427 CYTOCHROME B5 REDUCTASE B5R.2. [RefSeq;Acc:NM_016229] CYB5R2 0.497956 0.225776976
2200 0.11223 CYTOCHROME B5 REDUCTASE 1 (B5R.1). [RefSeq;Acc:NM_016243] CYB5R1 0.497084 0.22577673
2201 0.0966308 NADH-CYTOCHROME B5 REDUCTASE (EC 1.6.2.2) (B5R). [SWISSPROT;Acc:P00387] CYB5R3 0.427993 0.22577659
2202 0.0386224 HEPARIN SULFATE N-DEACETYLASE/N-SULFOTRANSFERASE (EC 2.8.2.-) (N- HSST) (N-HEPARIN SULFATE SULFOTRANSFERASE) (GLUCOSAMINYL N- DEACETYLASE/N-SULFOTRANSFERASE). [SWISSPROT;Acc:P52849] NDST2 0.17129 0.225479596
2203 0.0326359 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] NDST1 0.14474 0.22547948
2204 0.0316607 N-DEACETYLASE/N-SULFOTRANSFERASE (HEPARAN GLUCOSAMINYL) 3. [RefSeq;Acc:NM_004784] NDST3 0.140415 0.225479472
2205 0.0319117 N-DEACETYLASE/N-SULFOTRANSFERASE 4. [RefSeq;Acc:NM_022569] NDST4 0.141529 0.225478171
2206 0.244035 PROTEIN CDC27HS (CELL DIVISION CYCLE PROTEIN 27 HOMOLOG) (H-NUC). [SWISSPROT;Acc:P30260] CDC27 1.0823 0.225478148
2207 0.098654 SLC47A2 0.437657 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/