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 final Hugo
Results: HTML CSV LaTeX Showing element 2008 to 2057 of 3206 in total
Rank
description
measured
expected
final
Hugo
2008 "HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC 2 (EC 2.1.1.43) (HISTONE H3-K9 METHYLTRANSFERASE 2) (H3-K9-HMTASE 2) (SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 2) (SU(VAR)3-9 HOMOLOG 2). [SWISSPROT;Acc:Q9H5I1]" 0.0323264 0.14013 0.230688646 SUV39H2
2009 NUCLEOSIDE DIPHOSPHATE KINASE B (EC 2.7.4.6) (NDK B) (NDP KINASE B) (NM23-H2) (C-MYC PURINE-BINDING TRANSCRIPTION FACTOR PUF). [SWISSPROT;Acc:P22392] 0.533964 2.31472 0.230681897 no value
2010 NUCLEOSIDE DIPHOSPHATE KINASE A (EC 2.7.4.6) (NDK A) (NDP KINASE A) (TUMOR METASTATIC PROCESS-ASSOCIATED PROTEIN) (METASTASIS INHIBITION FACTOR NM23) (NM23-H1). [SWISSPROT;Acc:P15531] 0.494361 2.14316 0.230669199 NME2
2011 PUTATIVE NUCLEOSIDE DIPHOSPHATE KINASE (EC 2.7.4.6) (NDK) (NDP KINASE). [SWISSPROT;Acc:O60361] 0.480816 2.08449 0.230663616 NME2P1
2012 40S RIBOSOMAL PROTEIN S2 (S4) (LLREP3 PROTEIN). [SWISSPROT;Acc:P15880] 1.469 6.36963 0.230625641 no value
2013 PROTEIN ARGININE N-METHYLTRANSFERASE 3 (EC 2.1.1.-) (FRAGMENT). [SWISSPROT;Acc:O60678] 0.0198445 0.0860464 0.230625569 PRMT3
2014 60S RIBOSOMAL PROTEIN L23 (L17). [SWISSPROT;Acc:P23131] 0.64348 2.79016 0.230624767 no value
2015 BRCA2 AND CDKN1A-INTERACTING PROTEIN ISOFORM BCCIPALPHA; BRCA2 AND CDKN1A-INTERACTING PROTEIN; CDK INHIBITOR P21 BINDING PROTEIN; BCCIPALPHA; BCCIPBETA; TOK-1ALPHA; TOK-1BETA. [RefSeq;Acc:NM_016567] 0.0167203 0.0725001 0.230624509 BCCIP
2016 PUTATIVE EUKARYOTIC TRANSLATION INITIATION FACTOR 1A (EIF-1A) (EIF- 4C). [SWISSPROT;Acc:O75642] 1.27676 5.53686 0.230592791 no value
2017 "SUCCINATE DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN, MITOCHONDRIAL PRECURSOR (EC 1.3.5.1) (IP) (IRON-SULFUR SUBUNIT OF COMPLEX II). [SWISSPROT;Acc:P21912]" 0.311095 1.34923 0.230572252 SDHB
2018 40S RIBOSOMAL PROTEIN S16. [SWISSPROT;Acc:P17008] 0.590899 2.56327 0.230525462 RPS16
2019 "60S RIBOSOMAL PROTEIN L13, MITOCHONDRIAL (L13MT). [SWISSPROT;Acc:Q9BYD1]" MRPL13
2020 60S RIBOSOMAL PROTEIN L13A (23 KDA HIGHLY BASIC PROTEIN). [SWISSPROT;Acc:P40429] 0.587935 2.55045 0.230522065 RPL13A
2021 "LON PROTEASE HOMOLOG, MITOCHONDRIAL PRECURSOR (EC 3.4.21.-) (LON PROTEASE-LIKE PROTEIN) (LONP) (LONHS). [SWISSPROT;Acc:P36776]" 0.0840355 0.364571 0.230505169 no value
2022 0.123498 0.535804 0.230491 C11orf79
2023 "MAGUK P55 SUBFAMILY MEMBER 3 (MPP3 PROTEIN) (DISCS, LARGE HOMOLOG 3). [SWISSPROT;Acc:Q13368]" 0.112993 0.490447 0.230387789 MPP3
2024 TRANSKETOLASE (EC 2.2.1.1) (TK). [SWISSPROT;Acc:P29401] 0.150764 0.654499 0.230350237 TKT
2025 "PYRUVATE DEHYDROGENASE E1 COMPONENT ALPHA SUBUNIT, SOMATIC FORM, MITOCHONDRIAL PRECURSOR (EC 1.2.4.1) (PDHE1-A TYPE I). [SWISSPROT;Acc:P08559]" 0.38076 1.65321 0.230315568 PDHA1
2026 0.0327033 0.142004 0.230298442 C3orf23
2027 0.0370628 0.160934 0.230298135 SIN3B
2028 DENSITY-REGULATED PROTEIN (DRP) (DRP1 PROTEIN) (SMOOTH MUSCLE CELL ASSOCIATED PROTEIN-3) (SMAP-3). [SWISSPROT;Acc:O43583] 0.469395 2.03821 0.230297663 DENR
2029 "TRANSCRIPTIONAL CO-REPRESSOR SIN3A; TRANSCRIPTIONAL REGULATOR, SIN3A (YEAST). [RefSeq;Acc:NM_015477]" 0.0283438 0.123075 0.230296973 SIN3A
2030 "PYRUVATE DEHYDROGENASE E1 COMPONENT ALPHA SUBUNIT, TESTIS-SPECIFIC FORM, MITOCHONDRIAL PRECURSOR (EC 1.2.4.1) (PDHE1-A TYPE II). [SWISSPROT;Acc:P29803]" 0.353795 1.53626 0.230296304 PDHA2
2031 PROTEIN TRANSPORT PROTEIN SEC61 GAMMA SUBUNIT. [SWISSPROT;Acc:P38384] 0.114962 0.499271 0.230259719 SEC61G
2032 0.116403 0.505621 0.23021789 no value
2033 TRNA PSEUDOURIDINE SYNTHASE A (EC 4.2.1.70) (PSEUDOURIDYLATE SYNTHASE I) (PSEUDOURIDINE SYNTHASE I) (URACIL HYDROLYASE). [SWISSPROT;Acc:Q9Y606] 0.474475 2.06115 0.230199161 PUS1
2034 0.473995 2.05907 0.230198585 PUS3
2035 0.0841705 0.365653 0.230192286 DARS2
2036 40S RIBOSOMAL PROTEIN S5. [SWISSPROT;Acc:P46782] 1.08774 4.7257 0.230175424 RPS5
2037 CASEIN KINASE I ALPHA S-LIKE. [RefSeq;Acc:NM_145203] 0.0896146 0.389336 0.23017291 CSNK1A1L
2038 "CASEIN KINASE I, ALPHA ISOFORM (EC 2.7.1.-) (CKI-ALPHA) (CK1). [SWISSPROT;Acc:P48729]" 0.0909346 0.395071 0.230172804 CSNK1A1
2039 HUNTINGTIN INTERACTING PROTEIN 1 RELATED (HIP1-RELATED) (HIP 12). [SWISSPROT;Acc:O75146] 0.127824 0.555396 0.230149299 HIP1R
2040 "40S RIBOSOMAL PROTEIN S4, X ISOFORM (SINGLE COPY ABUNDANT MRNA PROTEIN) (SCR10). [SWISSPROT;Acc:P12750]" 0.707942 3.07604 0.230147202 no value
2041 "40S RIBOSOMAL PROTEIN S4, Y ISOFORM 2. [SWISSPROT;Acc:Q8TD47]" 0.667613 2.90083 0.23014551 RPS4Y2
2042 GOODPASTURE ANTIGEN-BINDING PROTEIN (EC 2.7.1.37) (GPBP) (COLLAGEN TYPE IV ALPHA 3 BINDING PROTEIN) (STAR-RELATED LIPID TRANSFER PROTEIN 11) (STARD11) (START DOMAIN-CONTAINING PROTEIN 11). [SWISSPROT;Acc:Q9Y5P4] 0.0646597 0.280961 0.230137635 COL4A3BP
2043 HUNTINGTIN INTERACTING PROTEIN 1 (HIP-I). [SWISSPROT;Acc:O00291] 0.104281 0.453153 0.230123159 HIP1
2044 DNA-DIRECTED RNA POLYMERASE II 14.5 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB9) (RPB14.5). [SWISSPROT;Acc:P36954] 0.110371 0.479632 0.230116006 POLR2I
2045 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM4 (GLYCINE-RICH PROTEIN) (GRP). [SWISSPROT;Acc:Q9Y4Z0] 0.308754 1.34189 0.230088904 LSM4
2046 DNA-DIRECTED RNA POLYMERASE I 40 KDA POLYPEPTIDE (EC 2.7.7.6) (RPA40) (RPA39). [SWISSPROT;Acc:O15160] 1.55851 6.77601 0.230004088 POLR1C
2047 INORGANIC PYROPHOSPHATASE 2 ISOFORM 1. [RefSeq;Acc:NM_176869] 0.123888 0.538763 0.229948976 PPA2
2048 AH RECEPTOR-INTERACTING PROTEIN (AIP) (IMMUNOPHILIN HOMOLOG ARA9) (HBV-X ASSOCIATED PROTEIN 2). [SWISSPROT;Acc:O00170] 0.052087 0.226516 0.229948436 AIP
2049 INORGANIC PYROPHOSPHATASE (EC 3.6.1.1) (PYROPHOSPHATE PHOSPHO- HYDROLASE) (PPASE). [SWISSPROT;Acc:Q15181] 0.128098 0.557073 0.229948319 PPA1
2050 ARYL-HYDROCARBON INTERACTING PROTEIN-LIKE 1. [SWISSPROT;Acc:Q9NZN9] 0.0410498 0.178518 0.22994768 AIPL1
2051 "COMPLEMENT COMPONENT 1, Q SUBCOMPONENT BINDING PROTEIN, MITOCHONDRIAL PRECURSOR (GLYCOPROTEIN GC1QBP) (GC1Q-R PROTEIN) (HYALURONAN-BINDING PROTEIN 1) (P32) (P33). [SWISSPROT;Acc:Q07021]" 0.532733 2.31678 0.229945442 C1QBP
2052 SIRTUIN 1; SIR2-LIKE 1; SIRTUIN TYPE 1; SIR2ALPHA; SIRTUIN SILENT MATING TYPE INFORMATION REGULATION 2 HOMOLOG 1 (S. CEREVISIAE). [RefSeq;Acc:NM_012238] 0.0404428 0.17588 0.229945417 SIRT1
2053 "SUCCINATE DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.3.5.1) (FP) (FLAVOPROTEIN SUBUNIT OF COMPLEX II). [SWISSPROT;Acc:P31040]" 0.150581 0.655122 0.229851844 SDHA
2054 0.0290537 0.126477 0.229715284 COQ10B
2055 "LIPOIC ACID SYNTHETASE, MITOCHONDRIAL (LIP-SYN) (LIPOATE SYNTHASE) (HUSSY-01) (FRAGMENT). [SWISSPROT;Acc:O43766]" 0.279023 1.21465 0.229714733 LIAS
2056 0.0315458 0.137326 0.229714694 COQ10A
2057 0.130459 0.567954 0.22969994 TKTL2

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/