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 [...,...].
Gene Hugo description Rank expected measured final
Results: HTML CSV LaTeX Showing element 201 to 250 of 3206 in total
Hugo  : no value
description
Rank
expected
measured
final
GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT-LIKE PROTEIN 12.3 (P205) (RECEPTOR OF ACTIVATED PROTEIN KINASE C 1) (RACK1) (RECEPTOR FOR ACTIVATED C KINASE). [SWISSPROT;Acc:P25388] 1504 0.461933 0.112103 0.24268238
GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-5 LIKE SUBUNIT. [SWISSPROT;Acc:Q9Y3K8] 3049 0.293231 0.0312821 0.10668074
GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-7 SUBUNIT. [SWISSPROT;Acc:O60262] 3042 0.366305 0.0391008 0.106743834
GUANINE NUCLEOTIDE-BINDING PROTEIN-LIKE 1 (GTP-BINDING PROTEIN HSR1). [SWISSPROT;Acc:P36915] 1287 0.527051 0.129655 0.246000861
HEAT SHOCK 70 KDA PROTEIN 1 (HSP70.1) (HSP70-1/HSP70-2). [SWISSPROT;Acc:P08107] 1772 0.277203 0.0654179 0.235992756
HEAT SHOCK FACTOR BINDING PROTEIN 1. [SWISSPROT;Acc:O75506] 508 0.493083 0.135095 0.273980243
HELICASE (FRAGMENT). [SPTREMBL;Acc:Q92771] 2767 1.60341 0.324046 0.202098029
HEPATITIS C VIRUS CORE-BINDING PROTEIN 6; CERVICAL CANCER ONCOGENE 3. [RefSeq;Acc:NM_023934] 2592 0.120086 0.0255653 0.212891594
HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN HCA1. [RefSeq;Acc:NM_020932] 3138 1.02411 0.0669581 0.065381746
HEPATOMA-DERIVED GROWTH FACTOR-RELATED PROTEIN 2. [RefSeq;Acc:NM_032631] 2866 0.165297 0.0312313 0.188940513
HISTONE DEACETYLASE 2 (HD2). [SWISSPROT;Acc:Q92769] 712 1.98825 0.52666 0.264886206
HISTONE H2B. [RefSeq;Acc:NM_175055] 1371 0.385154 0.0943097 0.244862315
HISTONE H2B.D (H2B/D). [SWISSPROT;Acc:Q99877] 1365 0.390892 0.0957148 0.24486252
HISTONE H2B.E (H2B/E). [SWISSPROT;Acc:Q99879] 1367 0.384945 0.0942586 0.244862513
HISTONE H2B.S (H2B/S). [SWISSPROT;Acc:P57053] 1370 0.386406 0.0946163 0.244862399
HISTONE H3.1 (H3/A) (H3/C) (H3/D) (H3/F) (H3/H) (H3/I) (H3/J) (H3/K) (H3/L). [SWISSPROT;Acc:P16106] 1368 0.641454 0.157068 0.244862453
HISTONE H3.3 (H3.A) (H3.B) (H3.3Q). [SWISSPROT;Acc:P06351] 1539 0.906671 0.21933 0.241906932
HISTONE H4. [SWISSPROT;Acc:P02304] 1913 0.35711 0.0828779 0.232079471
HOMEOBOX PROTEIN HOX-A4 (HOX-1D) (HOX-1.4). [SWISSPROT;Acc:Q00056] 2983 0.222701 0.0310799 0.13955887
HOMEOBOX PROTEIN HOX-C4 (HOX-3E) (CP19). [SWISSPROT;Acc:P09017] 2976 0.223469 0.0311872 0.139559402
HOMEOBOX PROTEIN HOX-C6 (HOX-3C) (HHO.C8) (CP25). [SWISSPROT;Acc:P09630] 2978 0.221164 0.0308655 0.139559332
HPAII TINY FRAGMENTS LOCUS 9C. [RefSeq;Acc:NM_022727] 303 0.697153 0.20849 0.299059174
HUNTINGTIN INTERACTING PROTEIN E; HUNTINGTIN INTERACTOR PROTEIN E. [RefSeq;Acc:NM_007076] 1003 0.110551 0.0281805 0.254909499
HUNTINGTIN-ASSOCIATED PROTEIN-INTERACTING PROTEIN (DUO PROTEIN). [SWISSPROT;Acc:O60229] 777 0.216002 0.0568574 0.263226266
HUNTINGTIN-INTERACTING PROTEIN HYPA/FBP11 (FRAGMENT). [SPTREMBL;Acc:O75404] 160 1.16002 0.40616 0.350131894
HURPIN (HACAT UV-REPRESSIBLE SERPIN) (PROTEASE INHIBITOR 13) (HEADPIN) (SERPIN B13). [SWISSPROT;Acc:Q9UIV8] 1584 0.271247 0.0653411 0.240891512
HYDROXYINDOLE O-METHYLTRANSFERASE (EC 2.1.1.4) (HIOMT) (ACETYLSEROTONIN O-METHYLTRANSFERASE) (ASMT). [SWISSPROT;Acc:P46597] 2117 1.11232 0.253802 0.228173547
IMPORTIN 4. [RefSeq;Acc:NM_024658] 1253 2.31408 0.572386 0.247349271
IMPORTIN 7; RAN-BINDING PROTEIN 7. [RefSeq;Acc:NM_006391] 1495 0.15167 0.036822 0.242777082
INTEGRAL MEMBRANE PROTEIN CII-3B. [SPTREMBL;Acc:O75609] 1995 0.959291 0.221383 0.230777731
INTERLEUKIN-1 RECEPTOR-ASSOCIATED KINASE 4; INTERLEUKIN-1 RECEPTOR ASSOCIATED KINASE 4. [RefSeq;Acc:NM_016123] 134 0.826637 0.290469 0.351386401
INTERSECTIN 1 (SH3 DOMAIN-CONTAINING PROTEIN 1A) (SH3P17). [SWISSPROT;Acc:Q15811] 1019 0.365399 0.0927584 0.253855101
INTERSECTIN 2 (SH3 DOMAIN-CONTAINING PROTEIN 1B) (SH3P18) (SH3P18-LIKE WASP ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q9NZM3] 1015 0.314025 0.079717 0.253855585
ISCHEMIA/REPERFUSION INDUCIBLE PROTEIN. [RefSeq;Acc:NM_024640] 1260 0.404396 0.0999509 0.247160951
JUN DIMERIZATION PROTEIN. [RefSeq;Acc:NM_130469] 230 0.614336 0.193648 0.315215127
KAPPA B-RAS 1. [RefSeq;Acc:NM_020345] 1273 0.155989 0.0384625 0.246571874
KERATIN ASSOCIATED PROTEIN 1-3; KERATIN ASSOCIATED PROTEIN 1.3. [RefSeq;Acc:NM_030966] 2531 0.120439 0.0258656 0.214760999
KERATIN ASSOCIATED PROTEIN 1.5. [RefSeq;Acc:NM_031957] 2532 0.116288 0.0249741 0.214760766
KERATIN ASSOCIATED PROTEIN 2-4; KERATIN ASSOCIATED PROTEIN 2.4. [RefSeq;Acc:NM_033184] 2533 0.112137 0.0240826 0.214760516
KERATIN ASSOCIATED PROTEIN 4-10; KERATIN ASSOCIATED PROTEIN 4.10. [RefSeq;Acc:NM_033060] 2529 0.130722 0.0280741 0.214761861
KERATIN ASSOCIATED PROTEIN 4-12; KERATIN ASSOCIATED PROTEIN 4.12. [RefSeq;Acc:NM_031854] 2521 0.19742 0.042399 0.214765475
KERATIN ASSOCIATED PROTEIN 4-14; KERATIN ASSOCIATED PROTEIN 4.14. [RefSeq;Acc:NM_033059] 2526 0.178175 0.0382656 0.214764136
KERATIN ASSOCIATED PROTEIN 4-2; KERATIN ASSOCIATED PROTEIN 4.2. [RefSeq;Acc:NM_033062] 2528 0.146383 0.0314375 0.21476196
KERATIN ASSOCIATED PROTEIN 4.3 (FRAGMENT). [SPTREMBL;Acc:Q9BYR4] 2534 0.121383 0.0260682 0.214759892
KERATIN ASSOCIATED PROTEIN 4.9 (FRAGMENT). [SPTREMBL;Acc:Q9BYQ8] 2525 0.178458 0.0383264 0.214764258
KERATIN ASSOCIATED PROTEIN 9-4; KERATIN ASSOCIATED PROTEIN 9.4. [RefSeq;Acc:NM_033191] 2502 4.7857 1.02862 0.214936164
KINESIN-LIKE PROTEIN KIF13B (KINESIN-LIKE PROTEIN GAKIN). [SWISSPROT;Acc:Q9NQT8] 852 0.250194 0.0651843 0.260535025
LAMIN B2. [SWISSPROT;Acc:Q03252] 1264 1.95026 0.481793 0.247040395
LARGE PROLINE-RICH PROTEIN BAT3 (HLA-B-ASSOCIATED TRANSCRIPT 3) (G3). [SWISSPROT;Acc:P46379] 2446 0.502445 0.109079 0.217096399
LIM DOMAIN BINDING 1; CARBOXY TERMINAL LIM DOMAIN PROTEIN 2; LIM DOMAIN-BINDING FACTOR-1. [RefSeq;Acc:NM_003893] 2079 0.427723 0.0979801 0.229073723

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/