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 [...,...].
measured Gene Rank Hugo description expected final
Results: HTML CSV LaTeX Showing element 252 to 301 of 3206 in total
measured
Rank
Hugo
description
expected
final
0.029 3201 RRAGC RAS-RELATED GTP BINDING C; RAG C PROTEIN. [RefSeq;Acc:NM_022157] 1.21378 0.023892303
0.0290537 2054 COQ10B 0.126477 0.229715284
0.0291377 2241 KIAA1033 0.130208 0.223778109
0.0292681 2971 TBCC TUBULIN-SPECIFIC CHAPERONE C (TUBULIN-FOLDING COFACTOR C) (CFC). [SWISSPROT;Acc:Q15814] 0.208597 0.140309305
2972 DDX43 DEAD-BOX PROTEIN. [RefSeq;Acc:NM_018665]
0.0293247 3050 GNG11 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-11 SUBUNIT. [SWISSPROT;Acc:P50152] 0.274937 0.106659707
0.0294363 2871 HDGFL1 PWWP DOMAIN CONTAINING 1; HDGF (HEPATOMA-DERIVED GROWTH FACTOR) LIKE. [RefSeq;Acc:NM_138574] 0.155797 0.188940095
0.0295551 2900 GATAD2B TRANSCRIPTION REPRESSOR P66 BETA COMPONENT OF THE MECP1 COMPLEX. [RefSeq;Acc:NM_020699] 0.169175 0.174701345
0.0295892 2336 C1orf50 0.133775 0.22118632
0.029603 2002 no value 0.128294 0.230743449
0.0296502 745 BA508N22.1 (HSPC025) (FRAGMENT). [SPTREMBL;Acc:Q9HCW5] 0.1121 0.26449777
0.0296703 817 NDUFS6 "NADH-UBIQUINONE OXIDOREDUCTASE 13 KDA-A SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-13KD-A) (CI-13KD-A). [SWISSPROT;Acc:O75380]" 0.113537 0.261327144
818 MYL6 "MYOSIN LIGHT CHAIN 1, SLOW-TWITCH MUSCLE A ISOFORM (MLC1SA) (ALKALI). [SWISSPROT;Acc:P14649]"
0.0296714 1549 ARL4A ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 4. [SWISSPROT;Acc:P40617] 0.122715 0.241791142
0.0297305 2268 LTA4H LEUKOTRIENE A-4 HYDROLASE (EC 3.3.2.6) (LTA-4 HYDROLASE) (LEUKOTRIENE A(4) HYDROLASE). [SWISSPROT;Acc:P09960] 0.133476 0.222740418
0.0297584 1321 TXN THIOREDOXIN (ATL-DERIVED FACTOR) (ADF) (SURFACE ASSOCIATED SULPHYDRYL PROTEIN) (SASP). [SWISSPROT;Acc:P10599] 0.121182 0.245567824
0.0298281 827 no value PUTATIVE ANKYRIN-REPEAT CONTAINING PROTEIN. [RefSeq;Acc:NM_025185] 0.114163 0.261276421
0.0298356 2112 DPY19L2 0.130757 0.228175929
0.0298377 2415 SERINC3 TUMOR DIFFERENTIALLY EXPRESSED PROTEIN 1 (TRANSMEMBRANE PROTEIN SBBI99). [SWISSPROT;Acc:Q13530] 0.136653 0.218346469
2416 MAF1 HOMOLOG OF YEAST MAF1. [RefSeq;Acc:NM_032272]
0.0299559 1758 DDX39 "DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 39 ISOFORM 1; NUCLEAR RNA HELICASE, DECD VARIANT OF DEAD BOX FAMILY. [RefSeq;Acc:NM_005804]" 0.126548 0.236715713
0.0299629 828 STARD3NL MLN64 N-TERMINAL DOMAIN HOMOLOG (STARD3 N-TERMINAL LIKE PROTEIN). [SWISSPROT;Acc:O95772] 0.114679 0.261276258
0.0299967 1818 ANK3 ANKYRIN 3 (ANK-3) (ANKYRIN G). [SWISSPROT;Acc:Q12955] 0.128045 0.234266859
0.0300014 822 FAT2 PROTOCADHERIN FAT 2 PRECURSOR (HFAT2) (MULTIPLE EPIDERMAL GROWTH FACTOR-LIKE DOMAINS 1). [SWISSPROT;Acc:Q9NYQ8] 0.114826 0.261277063
0.0302145 1114 CPXM2 POTENTIAL CARBOXYPEPTIDASE-LIKE PROTEIN X2 PRECURSOR. [SWISSPROT;Acc:Q8N436] 0.120464 0.250817672
1115 CPXM1 POTENTIAL CARBOXYPEPTIDASE X PRECURSOR (EC 3.4.17.-) (METALLOCARBOXYPEPTIDASE CPX-1). [SWISSPROT;Acc:Q96SM3]
0.0303013 1715 GTF2F1 "TRANSCRIPTION INITIATION FACTOR IIF, ALPHA SUBUNIT (TFIIF-ALPHA) (TRANSCRIPTION INITIATION FACTOR RAP74). [SWISSPROT;Acc:P35269]" 0.127662 0.237355674
0.0303497 830 KHK KETOHEXOKINASE (EC 2.7.1.3) (HEPATIC FRUCTOKINASE). [SWISSPROT;Acc:P50053] 0.116238 0.26109964
0.0303657 1795 ATP5S "ATP SYNTHASE COUPLING FACTOR B, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:Q99766]" 0.129305 0.234837787
0.0303816 1111 CPZ CPZ GENE PRODUCT. [RefSeq;Acc:NM_003652] 0.12113 0.250818129
0.0303893 1421 TBL1Y "TRANSDUCIN BETA-LIKE 1Y PROTEIN (TRANSDUCIN-BETA-LIKE 1, Y-LINKED). [SWISSPROT;Acc:Q9BQ87]" 0.1246 0.243894864
0.0303966 1793 COQ3 "HEXAPRENYLDIHYDROXYBENZOATE METHYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.1.114) (DIHYDROXYHEXAPRENYLBENZOATE METHYLTRANSFERASE) (3,4- DIHYDROXY-5-HEXAPRENYLBENZOATE METHYLTRANSFERASE) (DHHB METHYLTRANSFERASE) (DHHB-MT) (DHHB-MTASE). [SWISSPRO" 0.129436 0.234838839
0.0305282 808 TMCC1 0.116515 0.2620109
0.0305539 1787 VBP1 PREFOLDIN SUBUNIT 3 (VON HIPPEL-LINDAU BINDING PROTEIN 1) (VHL BINDING PROTEIN-1) (VBP-1) (HIBBJ46). [SWISSPROT;Acc:Q15765] 0.129981 0.235064356
1788 UXT UXT PROTEIN (UBIQUITOUSLY EXPRESSED TRANSCRIPT PROTEIN) (HSPC024). [SWISSPROT;Acc:Q9UBK9]
0.0305909 1974 DAGLB KCCR13L. [RefSeq;Acc:NM_139179] 0.13236 0.231118918
0.0305968 1189 ATP13A2 PROBABLE CATION-TRANSPORTING ATPASE 1 (EC 3.6.1.-). [SWISSPROT;Acc:Q9NQ11] 0.123075 0.248602884
0.0305978 1112 CPN1 CARBOXYPEPTIDASE N CATALYTIC CHAIN PRECURSOR (EC 3.4.17.3) (ARGININE CARBOXYPEPTIDASE) (KININASE 1) (SERUM CARBOXYPEPTIDASE N) (SCPN) (ANAPHYLATOXIN INACTIVATOR) (PLASMA CARBOXYPEPTIDASE B). [SWISSPROT;Acc:P15169] 0.121992 0.250818086
0.0306345 1420 TBL1X "TRANSDUCIN BETA-LIKE 1X PROTEIN (TRANSDUCIN-BETA-LIKE 1, X-LINKED). [SWISSPROT;Acc:O60907]" 0.125605 0.243895546
0.0306863 3035 GTF2H1 TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX P62 SUBUNIT (BASIC TRANSCRIPTION FACTOR 62 KDA SUBUNIT) (BTF2-P62) (GENERAL TRANSCRIPTION FACTOR IIH POLYPEPTIDE 1). [SWISSPROT;Acc:P32780] 0.267389 0.114762761
0.0307397 1387 APOB APOLIPOPROTEIN B-100 PRECURSOR (APO B-100) [CONTAINS: APOLIPOPROTEIN B-48 (APO B-48)]. [SWISSPROT;Acc:P04114] 0.125741 0.244468391
0.0307477 2860 ORAI1 0.162737 0.188941052
0.0307532 2089 ARHGEF9 CDC42 GUANINE EXCHANGE FACTOR 9; HPEM-2 COLLYBISTIN. [RefSeq;Acc:NM_015185] 0.13446 0.228716347
0.0308129 2407 ITM2B INTEGRAL MEMBRANE PROTEIN 2B (TRANSMEMBRANE PROTEIN BRI) [CONTAINS: ABRI/ADAN AMYLOID PEPTIDE]. [SWISSPROT;Acc:Q9Y287] 0.140868 0.21873598
0.030826 1097 PGAM4 PUTATIVE PHOSPHOGLYCERATE MUTASE 3 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13). [SWISSPROT;Acc:Q8N0Y7] 0.122661 0.251310522
0.030828500000000002 2413 no value 0.141189 0.218349163
0.0308447 1481 0.126946 0.242974966
0.03085 2867 ORAI2 0.163279 0.188940403
0.0308655 2978 no value HOMEOBOX PROTEIN HOX-C6 (HOX-3C) (HHO.C8) (CP25). [SWISSPROT;Acc:P09630] 0.221164 0.139559332
0.0308872 2869 PSIP1 PC4 AND SFRS1 INTERACTING PROTEIN 2; PC4 AND SFRS1 INTERACTING PROTEIN 1; TRANSCRIPTIONAL COACTIVATOR P52/P75. [RefSeq;Acc:NM_033222] 0.163476 0.188940273

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/