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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 2002 to 2051 of 3206 in total
Rank
description
measured
expected
final
Hugo
2002 0.029603 0.128294 0.230743449 no value
2003 0.0937028 0.406091 0.230743356 TXNDC10
2004 MTO1 PROTEIN HOMOLOG (CGI-02). [SWISSPROT;Acc:Q9Y2Z2] 0.297474 1.2892 0.230743096 MTO1
2005 40S RIBOSOMAL PROTEIN S20. [SWISSPROT;Acc:P17075] 0.834926 3.6186 0.230731775 RPS20
2006 "HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC 1 (EC 2.1.1.43) (HISTONE H3-K9 METHYLTRANSFERASE 1) (H3-K9-HMTASE 1) (SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 1) (SU(VAR)3-9 HOMOLOG 1). [SWISSPROT;Acc:O43463]" 0.027437 0.118935 0.230689032 SUV39H1
2007 EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 1 (EUKARYOTIC TRANSLATION INITIATION FACTOR 2 ALPHA SUBUNIT) (EIF-2-ALPHA) (EIF- 2ALPHA) (EIF-2A). [SWISSPROT;Acc:P05198] 0.761536 3.30114 0.230688792 EIF2S1
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

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/