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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Hugo measured Gene Rank description expected final
Results: HTML CSV LaTeX Showing element 1 to 50 of 3206 in total
Hugo: 
\def\wcA{0.16666666666667\textwidth} \def\wcB{0.16666666666667\textwidth} \def\wcC{0.16666666666667\textwidth} \def\wcD{0.16666666666667\textwidth} \def\wcE{0.16666666666667\textwidth} \begin{longtable}{|c|c|c|c|c|} \hline \parbox{\wcA}{\vspace{3pt}\noindent measured\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent Rank\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent description\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent expected\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent final\vspace{3pt}}\\ \hline \hline \parbox{\wcA}{\vspace{3pt}\noindent 0.000173011\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 3206\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.7865\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.000219976\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.000178236\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 3204\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent ATLASTIN; GUANYLATE-BINDING PROTEIN 3. \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.81025\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.000219977\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0174991\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 1916\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent BIFUNCTIONAL 3'-PHOSPHOADENOSINE 5'-PHOSPHOSULFATE SYNTHETHASE 2 (PAPS SYNTHETHASE 2) (PAPSS 2) (SULFURYLASE KINASE 2) (SK2) (SK 2) [INCLUDES: SULFATE ADENYLYLTRANSFERASE (EC 2.7.7.4) (SULFATE ADENYLATE TRANSFERASE) (SAT) (ATP-SULFURYLASE); 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CERVICAL CANCER ONCOGENE 3. \vspace{3pt}}&&\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0258656\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 2531\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent KERATIN ASSOCIATED PROTEIN 1-3; KERATIN ASSOCIATED PROTEIN 1.3. \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.120439\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.214760999\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0258973\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 2375\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent THIAMIN PYROPHOSPHOKINASE 1; MOUSE THIAMIN PYROPHOSPHOKINASE HOMOLOG; THIAMINE PYROPHOSPHOKINASE. \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.117689\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.220048603\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0259096\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 820\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent "MYOSIN LIGHT CHAIN 1, EMBRYONIC MUSCLE/ATRIAL ISOFORM (PRO1957). \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.0991465\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.261326421\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0260682\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 2534\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent KERATIN ASSOCIATED PROTEIN 4.3 (FRAGMENT). \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.121383\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.214759892\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.027225\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 2077\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent PREFOLDIN SUBUNIT 6 (PROTEIN KE2). \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.118824\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.22912038\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0274494\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 1854\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.117581\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.233450983\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0275157\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 1855\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent PRESENILIN-LIKE PROTEIN 2 (EC 3.4.99.-) (SPPL2A PROTEIN). \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.117865\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.233450982\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0275762\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 1647\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.11537\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.23902401\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0280741\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 2529\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent KERATIN ASSOCIATED PROTEIN 4-10; KERATIN ASSOCIATED PROTEIN 4.10. \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.130722\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.214761861\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0281805\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 1003\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent HUNTINGTIN INTERACTING PROTEIN E; HUNTINGTIN INTERACTOR PROTEIN E. \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.110551\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.254909499\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0285187\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 659\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent SECRETED MODULAR CALCIUM-BINDING PROTEIN 1. \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.106766\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.267114063\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0286746\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 504\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent ENIGMA PROTEIN; LIM DOMAIN PROTEIN. \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.104626\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.274067631\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.028817\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 3187\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 14C; SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR-81; PKC-POTENTIATED PP1 INHIBITORY PROTEIN. \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.772261\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.037315105\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.029603\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 2002\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.128294\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.230743449\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0296502\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 745\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent BA508N22.1 (HSPC025) (FRAGMENT). \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.1121\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.26449777\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0298281\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 827\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent PUTATIVE ANKYRIN-REPEAT CONTAINING PROTEIN. \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.114163\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.261276421\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.030828500000000002\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 2413\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcC}{\vspace{3pt}\noindent \vspace{3pt}}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.141189\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.218349163\vspace{3pt}}\\\cline{1-2}\cline{4-5} \parbox{\wcA}{\vspace{3pt}\noindent 0.0308447\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 1481\vspace{3pt}}&&\parbox{\wcD}{\vspace{3pt}\noindent 0.126946\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.242974966\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0308655\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 2978\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent HOMEOBOX PROTEIN HOX-C6 (HOX-3C) (HHO.C8) (CP25). \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.221164\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.139559332\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0310375\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 811\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent BRAIN PROTEIN 16. \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.118668\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.261549028\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0310799\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 2983\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent HOMEOBOX PROTEIN HOX-A4 (HOX-1D) (HOX-1.4). \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.222701\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.13955887\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0311872\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 2976\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent HOMEOBOX PROTEIN HOX-C4 (HOX-3E) (CP19). \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.223469\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.139559402\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0312313\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 2866\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent HEPATOMA-DERIVED GROWTH FACTOR-RELATED PROTEIN 2. \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.165297\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.188940513\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0312821\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 3049\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-5 LIKE SUBUNIT. \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.293231\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.10668074\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.031325\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 2088\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcC}{\vspace{3pt}\noindent \vspace{3pt}}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.13696\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.228716414\vspace{3pt}}\\\cline{1-2}\cline{4-5} \parbox{\wcA}{\vspace{3pt}\noindent 0.0313747\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 2723\vspace{3pt}}&&\parbox{\wcD}{\vspace{3pt}\noindent 0.1519\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.206548387\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0314375\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 2528\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent KERATIN ASSOCIATED PROTEIN 4-2; KERATIN ASSOCIATED PROTEIN 4.2. \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.146383\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.21476196\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.031639\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 1423\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent NUCLEAR RECEPTOR CO-REPRESSOR/HDAC3 COMPLEX SUBUNIT TBLR1 (TBL1- RELATED PROTEIN 1). \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.129724\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.24389473\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0320499\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 2001\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent POLY (ADP-RIBOSE) GLYCOHYDROLASE. \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.138898\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.230744143\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0321572\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 752\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent LIPOPOLYSACCHARIDE-RESPONSIVE AND BEIGE-LIKE ANCHOR PROTEIN (CDC4-LIKE PROTEIN) (BEIGE-LIKE PROTEIN). \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.121579\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.264496336\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0322794\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 1099\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent PHOSPHOGLYCERATE MUTASE 1 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13) (PHOSPHOGLYCERATE MUTASE ISOZYME B) (PGAM-B) (BPG-DEPENDENT PGAM 1). \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.128445\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.251309121\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 0.0331615\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 1852\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent PRESENILIN-LIKE PROTEIN 1 (EC 3.4.99.-) (SPPL2B PROTEIN). \vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 0.142049\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 0.233451133\vspace{3pt}}\\\hline nd{longtable}
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/