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 302 to 350 of 350 in total
Hugo  : no value
Rank
description
measured
expected
final
2723 0.0313747 0.1519 0.206548387
2725 0.10808 0.525053 0.205845886
2767 HELICASE (FRAGMENT). [SPTREMBL;Acc:Q92771] 0.324046 1.60341 0.202098029
2768 ZINC FINGER PROTEIN 277. [SWISSPROT;Acc:Q9NRM2] 0.0570468 0.282946 0.20161727
2769 SIMILAR TO ZINC FINGER PROTEIN 277. [SPTREMBL;Acc:Q8WWA6] 0.0486609 0.241353 0.201617133
2773 DJ570F3.6 (NOVEL PROTEIN SIMILAR TO LYSOPHOSPHOLIPASE II (LYPLA2)). [SPTREMBL;Acc:Q9UGE0] 0.0202703 0.100647 0.201399942
2799 "ATAXIN 2; OLIVOPONTOCEREBELLAR ATAXIA 2, AUTOSOMAL DOMINANT. [RefSeq;Acc:NM_002973]" 0.0572133 0.287777 0.198811232
2807 0.101691 0.514373 0.197698946
2827 ZINC FINGER IMPRINTED 2. [SWISSPROT;Acc:Q9NZV7] 0.161283 0.833576 0.193483258
2835 "SUCCINATE DEHYDROGENASE [UBIQUINONE] CYTOCHROME B SMALL SUBUNIT, MITOCHONDRIAL PRECURSOR (CYBS) (SUCCINATE-UBIQUINONE REDUCTASE MEMBRANE ANCHOR SUBUNIT) (QPS2) (CII-4) (SUCCINATE DEHYDROGENASE COMPLEX SUBUNIT D) (SUCCINATE-UBIQUINONE OXIDOREDUCTASE CYTOCH" 0.0431276 0.223379 0.193069178
2852 SMALL GLUTAMINE RICH PROTEIN WITH TETRATRICOPEPTIDE REPEATS 2. [RefSeq;Acc:NM_019072] 0.839834 4.39067 0.191276958
2859 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE ALPHA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 1) (1-AGPAT 1) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-ALPHA) (LPAAT-ALPHA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 1) (G15 PROTEIN). [SWISSPROT;Acc:Q9 0.246538 1.30479 0.188948413
2862 CGI-142; HEPATOMA-DERIVED GROWTH FACTOR 2. [RefSeq;Acc:NM_016073] 0.0372023 0.196899 0.188941031
2866 HEPATOMA-DERIVED GROWTH FACTOR-RELATED PROTEIN 2. [RefSeq;Acc:NM_032631] 0.0312313 0.165297 0.188940513
2872 0.0371369 0.196598 0.188897649
2878 RET FINGER PROTEIN 2 (LEUKEMIA ASSOCIATED PROTEIN 5) (B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA TUMOR SUPPRESSOR LEU5) (PUTATIVE TUMOR SUPPRESSOR RFP2) (TRIPARTITE MOTIF PROTEIN 13). [SWISSPROT;Acc:O60858] 0.101998 0.546053 0.186791392
2881 ADAPTER-RELATED PROTEIN COMPLEX 3 BETA 2 SUBUNIT (BETA-ADAPTIN 3B) (AP-3 COMPLEX BETA-3B SUBUNIT) (BETA-3B-ADAPTIN) (NEURON-SPECIFIC VESICLE COAT PROTEIN BETA-NAP). [SWISSPROT;Acc:Q13367] 0.0513128 0.278146 0.184481531
2892 UBIQUITIN ACTIVATING ENZYME E1-LIKE PROTEIN. [RefSeq;Acc:NM_006395] 0.151451 0.850269 0.178121277
2902 TYROSINE AMINOTRANSFERASE (EC 2.6.1.5) (L-TYROSINE:2-OXOGLUTARATE AMINOTRANSFERASE) (TAT). [SWISSPROT;Acc:P17735] 0.174557 0.999179 0.174700429
2903 60S RIBOSOMAL PROTEIN L22 (EPSTEIN-BARR VIRUS SMALL RNA ASSOCIATED PROTEIN) (EBER ASSOCIATED PROTEIN) (EAP) (HEPARIN BINDING PROTEIN HBP15). [SWISSPROT;Acc:P35268] 0.173712 0.997527 0.174142655
2920 UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 3 (EC 6.3.2.19) (UBIQUITIN- PROTEIN LIGASE) (UBIQUITIN CARRIER PROTEIN) (E2(17)KB 3). [SWISSPROT;Acc:P47986] 0.126707 0.750535 0.16882224
2921 PNAS-18. [SPTREMBL;Acc:Q9BZU3] 0.304269 1.80704 0.168379781
2923 CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT 1 (CKS-1) (SID1334) (PNAS-16 / PNAS-143). [SWISSPROT;Acc:P33551] 0.363846 2.16723 0.167885273
2960 RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR-LIKE 2 (RALGDS-LIKE FACTOR) (RAS-ASSOCIATED PROTEIN RAB2L). [SWISSPROT;Acc:O15211] 0.0746316 0.510598 0.146165085
2962 TRANSFORMING PROTEIN N-RAS. [SWISSPROT;Acc:P01111] 0.217355 1.48707 0.146163261
2976 HOMEOBOX PROTEIN HOX-C4 (HOX-3E) (CP19). [SWISSPROT;Acc:P09017] 0.0311872 0.223469 0.139559402
2978 HOMEOBOX PROTEIN HOX-C6 (HOX-3C) (HHO.C8) (CP25). [SWISSPROT;Acc:P09630] 0.0308655 0.221164 0.139559332
2983 HOMEOBOX PROTEIN HOX-A4 (HOX-1D) (HOX-1.4). [SWISSPROT;Acc:Q00056] 0.0310799 0.222701 0.13955887
3001 GABA-A RECEPTOR-ASSOCIATED PROTEIN. [SPTREMBL;Acc:Q9BY60] 0.0506272 0.392576 0.128961526
3004 ENDO-BETA-N-ACETYLGLUCOSAMINIDASE. [RefSeq;Acc:NM_022759] 0.0444453 0.352603 0.126049126
3024 SYNBINDIN (TRS23 HOMOLOG) (HEMATOPOIETIC STEM/PROGENITOR CELL PROTEIN 172) (HSPC172) (PTD009) (CGI-104). [SWISSPROT;Acc:Q9Y296] 0.0250043 0.209553 0.119322081
3034 TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX P44 SUBUNIT (BASIC TRANSCRIPTION FACTOR 2 44 KDA SUBUNIT) (BTF2-P44) (GENERAL TRANSCRIPTION FACTOR IIH POLYPEPTIDE 2). [SWISSPROT;Acc:Q13888] 0.146213 1.27404 0.114763273
3042 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-7 SUBUNIT. [SWISSPROT;Acc:O60262] 0.0391008 0.366305 0.106743834
3049 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-5 LIKE SUBUNIT. [SWISSPROT;Acc:Q9Y3K8] 0.0312821 0.293231 0.10668074
3069 0.0533885 0.517345 0.103197093
3090 METHYLTRANSFERASE LIKE 2. [RefSeq;Acc:NM_018396] 0.048624 0.498014 0.097635809
3109 "MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE IB (EC 3.2.1.113) (PROCESSING ALPHA-1,2-MANNOSIDASE IB) (ALPHA-1,2-MANNOSIDASE IB) (MANNOSIDASE ALPHA CLASS 1A MEMBER 2). [SWISSPROT;Acc:O60476]" 0.116081 1.26306 0.091904581
3123 NUCLEAR DNA-BINDING PROTEIN; SMALL UNIQUE NUCLEAR RECEPTOR COREPRESSOR; C1D DNA-BINDING PROTEIN. [RefSeq;Acc:NM_006333] 0.0678638 0.874459 0.077606612
3131 "MYOSIN VA (MYOSIN 5A) (DILUTE MYOSIN HEAVY CHAIN, NON-MUSCLE) (MYOSIN HEAVY CHAIN 12) (MYOXIN). [SWISSPROT;Acc:Q9Y4I1]" 0.163856 2.39209 0.068499095
3138 HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN HCA1. [RefSeq;Acc:NM_020932] 0.0669581 1.02411 0.065381746
3147 MELANOMA-ASSOCIATED ANTIGEN 1 (MAGE-1 ANTIGEN) (ANTIGEN MZ2-E). [SWISSPROT;Acc:P43355] 0.0648148 0.99133 0.065381659
3148 MELANOMA-ASSOCIATED ANTIGEN 3 (MAGE-3 ANTIGEN) (ANTIGEN MZ2-D). [SWISSPROT;Acc:P43357] 0.0646293 0.988493 0.065381647
3149 MELANOMA-ASSOCIATED ANTIGEN 4 (MAGE-4 ANTIGEN) (MAGE-X2) (MAGE-41). [SWISSPROT;Acc:P43358] 0.0651239 0.996058 0.065381634
3163 "MYOSIN HEAVY CHAIN, CARDIAC MUSCLE BETA ISOFORM (MYHC-BETA). [SWISSPROT;Acc:P12883]" 0.0816437 1.26168 0.064710307
3166 "MYOSIN HEAVY CHAIN, CARDIAC MUSCLE ALPHA ISOFORM (MYHC-ALPHA). [SWISSPROT;Acc:P13533]" 0.081705 1.26263 0.064710168
3169 RIBOSOMAL PROTEIN S6 KINASE-LIKE 1. [RefSeq;Acc:NM_031464] 0.038917 0.619812 0.062788394
3187 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 14C; SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR-81; PKC-POTENTIATED PP1 INHIBITORY PROTEIN. [RefSeq;Acc:NM_030949]" 0.028817 0.772261 0.037315105
3204 ATLASTIN; GUANYLATE-BINDING PROTEIN 3. [RefSeq;Acc:NM_015915] 0.000178236 0.81025 0.000219977
3206 0.000173011 0.7865 0.000219976

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/