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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expected Gene Rank description measured final Hugo
Results: HTML CSV LaTeX Showing element 252 to 301 of 3206 in total
expected
Rank
description
measured
final
Hugo
0.125741 1387 APOLIPOPROTEIN B-100 PRECURSOR (APO B-100) [CONTAINS: APOLIPOPROTEIN B-48 (APO B-48)]. [SWISSPROT;Acc:P04114] 0.0307397 0.244468391 APOB
0.125928 2210 NUCLEOBINDIN 2 PRECURSOR (DNA-BINDING PROTEIN NEFA). [SWISSPROT;Acc:P80303] 0.0283406 0.225053999 NUCB2
0.126112 1262 0.0311675 0.24714143 SHQ1
0.126186 925 FATTY ACID DESATURASE 3; LINOLEOYL-COA DESATURASE (DELTA-6-DESATURASE)-LIKE 3; DELTA-6 FATTY ACID DESATURASE. [RefSeq;Acc:NM_021727] 0.0325155 0.25767914 FADS3
0.126477 2054 0.0290537 0.229715284 COQ10B
0.126548 1758 "DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 39 ISOFORM 1; NUCLEAR RNA HELICASE, DECD VARIANT OF DEAD BOX FAMILY. [RefSeq;Acc:NM_005804]" 0.0299559 0.236715713 DDX39
0.126718 2453 BRACHYURY PROTEIN (T PROTEIN). [SWISSPROT;Acc:O15178] 0.0274799 0.216858694 T
0.126926 592 "SPECTRIN BETA CHAIN, BRAIN 2 (SPECTRIN, NON-ERYTHROID BETA CHAIN 2) (BETA-III SPECTRIN). [SWISSPROT;Acc:O15020]" 0.0341846 0.269327009 SPTBN2
0.126946 1481 0.0308447 0.242974966 no value
0.127356 2544 COX15 HOMOLOG ISOFORM 2 PRECURSOR; CYTOCHROME C OXIDASE SUBUNIT 15; CYTOCHROME C OXIDASE ASSEMBLY PROTEIN. [RefSeq;Acc:NM_004376] 0.0273323 0.214613367 COX15
2545 FAM86B2
0.127549 2385 0.0280218 0.219694392 C14orf153
2386 MOLYBDENUM COFACTOR SYNTHESIS PROTEIN 2 LARGE SUBUNIT (MOLYBDOPTERIN SYNTHASE LARGE SUBUNIT) (MPT SYNTHASE LARGE SUBUNIT) (MOCS2B) (MOCO1- B). [SWISSPROT;Acc:O96007] MOCS2
2387 URM1
0.127662 1715 "TRANSCRIPTION INITIATION FACTOR IIF, ALPHA SUBUNIT (TFIIF-ALPHA) (TRANSCRIPTION INITIATION FACTOR RAP74). [SWISSPROT;Acc:P35269]" 0.0303013 0.237355674 GTF2F1
0.127753 282 "FATTY ACID-BINDING PROTEIN, BRAIN (B-FABP) (BRAIN LIPID-BINDING PROTEIN) (BLBP) (MAMMARY DERIVED GROWTH INHIBITOR RELATED). [SWISSPROT;Acc:O15540]" 0.0385572 0.301810525 FABP7
0.128045 1818 ANKYRIN 3 (ANK-3) (ANKYRIN G). [SWISSPROT;Acc:Q12955] 0.0299967 0.234266859 ANK3
0.128294 2002 0.029603 0.230743449 no value
0.128445 1099 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). [SWISSPROT;Acc:P18669] 0.0322794 0.251309121
0.12882 1092 3-OXO-5-ALPHA-STEROID 4-DEHYDROGENASE 2 (EC 1.3.99.5) (STEROID 5-ALPHA-REDUCTASE 2) (SR TYPE 2) (5 ALPHA-SR2). [SWISSPROT;Acc:P31213] 0.0324086 0.2515805 SRD5A2
0.128904 1406 CYTOCHROME C. [SWISSPROT;Acc:P00001] 0.0314533 0.244005617 CYCS
1407 HEPARAN SULFATE 6-O-SULFOTRANSFERASE; HEPARAN-SULFATE 6-SULFOTRANSFERASE. [RefSeq;Acc:NM_004807] HS6ST1
0.128948 1292 ECOTROPIC VIRAL INTEGRATION SITE 5; NEUROBLASTOMA STAGE 4S GENE. [RefSeq;Acc:NM_005665] 0.0317084 0.245900673 EVI5
0.12912 1268 SINGLE-MINDED HOMOLOG 1. [SWISSPROT;Acc:P81133] 0.0318532 0.246694548 SIM1
0.12923 1043 0.0327294 0.253264722 TMEM87B
0.129305 1795 "ATP SYNTHASE COUPLING FACTOR B, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:Q99766]" 0.0303657 0.234837787 ATP5S
0.129436 1793 "HEXAPRENYLDIHYDROXYBENZOATE METHYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.1.114) (DIHYDROXYHEXAPRENYLBENZOATE METHYLTRANSFERASE) (3,4- DIHYDROXY-5-HEXAPRENYLBENZOATE METHYLTRANSFERASE) (DHHB METHYLTRANSFERASE) (DHHB-MT) (DHHB-MTASE). [SWISSPRO" 0.0303966 0.234838839 COQ3
0.129486 1168 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 2 (SMAD 2) (MOTHERS AGAINST DPP HOMOLOG 2) (MAD-RELATED PROTEIN 2) (HMAD-2) (JV18-1) (HSMAD2). [SWISSPROT;Acc:Q15796] 0.0322934 0.249396846 SMAD2
0.129562 1422 0.0315995 0.243894815 PCID2
0.129724 1423 NUCLEAR RECEPTOR CO-REPRESSOR/HDAC3 COMPLEX SUBUNIT TBLR1 (TBL1- RELATED PROTEIN 1). [SWISSPROT;Acc:Q9BZK7] 0.031639 0.24389473 no value
0.129981 1787 PREFOLDIN SUBUNIT 3 (VON HIPPEL-LINDAU BINDING PROTEIN 1) (VHL BINDING PROTEIN-1) (VBP-1) (HIBBJ46). [SWISSPROT;Acc:Q15765] 0.0305539 0.235064356 VBP1
1788 UXT PROTEIN (UBIQUITOUSLY EXPRESSED TRANSCRIPT PROTEIN) (HSPC024). [SWISSPROT;Acc:Q9UBK9] UXT
0.130205 1601 TRANSLIN-ASSOCIATED PROTEIN X (TRANSLIN-ASSOCIATED FACTOR X). [SWISSPROT;Acc:Q99598] 0.0312503 0.240008448 TSNAX
1602 POLYGLUTAMINE BINDING PROTEIN 1; NUCLEAR PROTEIN CONTAINING WW DOMAIN 38 KD. [RefSeq;Acc:NM_005710] PQBP1
0.130208 2241 0.0291377 0.223778109 KIAA1033
0.130409 2344 "2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.2.4.4) (BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 COMPONENT ALPHA CHAIN) (BCKDH E1-ALPHA). [SWISSPROT;Acc:P12694]" 0.0287655 0.220579101 TMEM91
0.130706 928 FATTY ACID DESATURASE 2; LINOLEOYL-COA DESATURASE (DELTA-6-DESATURASE)-LIKE 2; DELTA-6 FATTY ACID DESATURASE. [RefSeq;Acc:NM_004265] 0.0336801 0.257678301 FADS2
0.130722 2529 KERATIN ASSOCIATED PROTEIN 4-10; KERATIN ASSOCIATED PROTEIN 4.10. [RefSeq;Acc:NM_033060] 0.0280741 0.214761861 no value
0.130757 2112 0.0298356 0.228175929 DPY19L2
0.130845 333 GA BINDING PROTEIN BETA-2 CHAIN (GABP-BETA-2 SUBUNIT) (TRANSCRIPTION FACTOR E4TF1-47) (GAPBP-2) (NUCLEAR RESPIRATORY FACTOR-2 SUBUNIT GAMMA). [SWISSPROT;Acc:Q06545] 0.0373117 0.28515954 no value
0.130885 1169 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 3 (SMAD 3) (MOTHERS AGAINST DPP HOMOLOG 3) (MAD3) (HMAD-3) (MMAD3) (JV15-2) (HSMAD3). [SWISSPROT;Acc:Q92940] 0.0326423 0.249396799 SMAD3
0.131153 1696 "ADP,ATP CARRIER PROTEIN, LIVER ISOFORM T2 (ADP/ATP TRANSLOCASE 3) (ADENINE NUCLEOTIDE TRANSLOCATOR 3) (ANT 3). [SWISSPROT;Acc:P12236]" 0.0311972 0.237868749 SLC25A6
0.131347 203 POLYADENYLATE-BINDING PROTEIN 1 (POLY(A)-BINDING PROTEIN 1) (PABP 1). [SWISSPROT;Acc:P11940] 0.0422886 0.321960913 PABPC1
0.131474 1020 HIV TAT SPECIFIC FACTOR 1; COFACTOR REQUIRED FOR TAT ACTIVATION OF HIV-1 TRANSCRIPTION. [RefSeq;Acc:NM_014500] 0.0333753 0.253854755 HTATSF1
0.131705 949 "OLIGORIBONUCLEASE, MITOCHONDRIAL PRECURSOR (EC 3.1.-.-) (SMALL FRAGMENT NUCLEASE) (CGI-114). [SWISSPROT;Acc:Q9Y3B8]" 0.0337699 0.256405603 REXO2
0.131824 831 "MALONYL-COA DECARBOXYLASE, MITOCHONDRIAL PRECURSOR (EC 4.1.1.9) (MCD). [SWISSPROT;Acc:O95822]" 0.0344093 0.261024548 MLYCD
0.132186 1446 SPERMIDINE SYNTHASE (EC 2.5.1.16) (PUTRESCINE AMINOPROPYLTRANSFERASE) (SPDSY). [SWISSPROT;Acc:P19623] 0.032182 0.243459973 SRM
0.132289 2557 METABOTROPIC GLUTAMATE RECEPTOR 2 PRECURSOR (MGLUR2). [SWISSPROT;Acc:Q14416] 0.0283513 0.214313359 GRM2
0.13229 540 0.0358609 0.271077935 LRRC4B
0.13236 1974 KCCR13L. [RefSeq;Acc:NM_139179] 0.0305909 0.231118918 DAGLB

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/