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 [...,...].
Hugo expected measured Gene Rank description final
Results: HTML CSV LaTeX Showing element 101 to 150 of 3206 in total
Hugo  : no value
expected
measured
Rank
description
final
0.223469 0.0311872 2976 HOMEOBOX PROTEIN HOX-C4 (HOX-3E) (CP19). [SWISSPROT;Acc:P09017] 0.139559402
0.227574 0.0568291 1151 SPROUTY HOMOLOG 4 (SPRY-4). [SWISSPROT;Acc:Q9C004] 0.249717015
0.231274 0.0637349 460 COLLAGEN ALPHA 5(IV) CHAIN PRECURSOR. [SWISSPROT;Acc:P29400] 0.27558177699999997
0.238723 0.0511995 2553 0.214472422
0.239562 0.0544712 2148 APOPTOSIS INHIBITOR FKSG2. [SWISSPROT;Acc:Q9HAU6] 0.227378299
0.240043 0.0614814 960 "ACYL-COA DEHYDROGENASE, SHORT/BRANCHED CHAIN SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 1.3.99.-) (SBCAD) (2-METHYL BRANCHED CHAIN ACYL-COA DEHYDROGENASE) (2-MEBCAD) (2-METHYLBUTYRYL-COENZYME A DEHYDROGENASE) (2-METHYLBUTYRYL-COA DEHYDROGENASE). [SWISSP" 0.256126611
0.241075 0.0573148 1704 DJ408B20.3 (NOVEL PROTEIN SIMILAR TO 60S ACIDIC RIBOSOMAL PROTEIN P2 (RPLP2)). [SPTREMBL;Acc:Q9H5A9] 0.237746759
0.241353 0.0486609 2769 SIMILAR TO ZINC FINGER PROTEIN 277. [SPTREMBL;Acc:Q8WWA6] 0.201617133
0.247068 0.0571361 1953 60S RIBOSOMAL PROTEIN L14 (CAG-ISL 7). [SWISSPROT;Acc:P50914] 0.231256577
0.247338 0.0580492 1800 0.234695841
0.250194 0.0651843 852 KINESIN-LIKE PROTEIN KIF13B (KINESIN-LIKE PROTEIN GAKIN). [SWISSPROT;Acc:Q9NQT8] 0.260535025
0.250685 0.0569865 2151 STEROL REGULATORY ELEMENT BINDING PROTEIN-2 (SREBP-2) (STEROL REGULATORY ELEMENT-BINDING TRANSCRIPTION FACTOR 2). [SWISSPROT;Acc:Q12772] 0.227323135
0.25292 0.0671866 688 SIGNAL-INDUCED PROLIFERATION-ASSOCIATED 1-LIKE 1. [RefSeq;Acc:NM_015556] 0.265643682
0.254478 0.0589414 1940 "ISOLEUCYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.5) (ISOLEUCINE--TRNA LIGASE) (ILERS) (IRS). [SWISSPROT;Acc:P41252]" 0.231616878
0.257167 0.0607427 1764 0.236199435
0.263425 0.0697761 713 DJ153G14.2 (POSSIBLE CA BINDING PROTEIN SIMILAR TO NEFA) (FRAGMENT). [SPTREMBL;Acc:Q9UJN8] 0.264880326
0.26352 0.0561617 2582 BLOOD GROUP RH(CE) POLYPEPTIDE (RHESUS C/E ANTIGENS) (RH30A) (RHIXB) (RH POLYPEPTIDE 1) (RHPI). [SWISSPROT;Acc:P18577] 0.213121205
0.264963 0.0564693 2580 0.213121455
0.270506 0.0577101 2574 0.213341294
0.271247 0.0653411 1584 HURPIN (HACAT UV-REPRESSIBLE SERPIN) (PROTEASE INHIBITOR 13) (HEADPIN) (SERPIN B13). [SWISSPROT;Acc:Q9UIV8] 0.240891512
0.274218 0.0604093 2366 PEPSIN A PRECURSOR (EC 3.4.23.1). [SWISSPROT;Acc:P00790] 0.220296625
0.277203 0.0654179 1772 HEAT SHOCK 70 KDA PROTEIN 1 (HSP70.1) (HSP70-1/HSP70-2). [SWISSPROT;Acc:P08107] 0.235992756
0.278146 0.0513128 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] 0.184481531
0.280704 0.0640341 2127 "GLYCINE DEHYDROGENASE [DECARBOXYLATING], MITOCHONDRIAL PRECURSOR (EC 1.4.4.2) (GLYCINE DECARBOXYLASE) (GLYCINE CLEAVAGE SYSTEM P- PROTEIN). [SWISSPROT;Acc:P23378]" 0.228119656
0.282946 0.0570468 2768 ZINC FINGER PROTEIN 277. [SWISSPROT;Acc:Q9NRM2] 0.20161727
0.287741 0.0700456 1448 BASIC PROLINE-RICH PEPTIDE P-E (IB-9). [SWISSPROT;Acc:P02811] 0.243432809
0.287777 0.0572133 2799 "ATAXIN 2; OLIVOPONTOCEREBELLAR ATAXIA 2, AUTOSOMAL DOMINANT. [RefSeq;Acc:NM_002973]" 0.198811232
0.28817 0.0739754 936 RHO INTERACTING PROTEIN 3. [RefSeq;Acc:NM_015134] 0.256707499
0.290115 0.061947 2565 TETRATRICOPEPTIDE REPEAT PROTEIN 4 (MY044 PROTEIN). [SWISSPROT;Acc:O95801] 0.213525671
0.29203 0.0637011 2423 TRANSCRIPTION ELONGATION FACTOR A PROTEIN 1 (TRANSCRIPTION ELONGATION FACTOR S-II PROTEIN 1) (TRANSCRIPTION ELONGATION FACTOR TFIIS.O). [SWISSPROT;Acc:P23193] 0.218132041
0.293231 0.0312821 3049 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-5 LIKE SUBUNIT. [SWISSPROT;Acc:Q9Y3K8] 0.10668074
0.302004 0.0733796 1475 RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 (P21-RAC1) (RAS-LIKE PROTEIN TC25). [SWISSPROT;Acc:P15154] 0.24297559
0.309407 0.0760628 1298 0.245834128
0.312352 0.0753661 1557 0.241285793
0.314025 0.079717 1015 INTERSECTIN 2 (SH3 DOMAIN-CONTAINING PROTEIN 1B) (SH3P18) (SH3P18-LIKE WASP ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q9NZM3] 0.253855585
0.318777 0.0884193 425 DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 47; HQP0256 PROTEIN. [RefSeq;Acc:NM_016355] 0.277370387
0.323509 0.0802494 1213 DYSTROPHIN. [SWISSPROT;Acc:P11532] 0.24805925
0.324228 0.0869771 626 0.268259065
0.33698 0.141847 32 PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC (EC 2.7.1.112) (P60-SRC) (C-SRC). [SWISSPROT;Acc:P12931] 0.420935961
0.338281 0.090945 614 DJ947L8.1.1 (NOVEL CUB AND SUSHI (SCR REPEAT) DOMAIN PROTEIN) (FRAGMENT). [SPTREMBL;Acc:Q9H4V7] 0.26884454
0.351165 0.0948257 582 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 55 KDA REGULATORY SUBUNIT B, ALPHA ISOFORM (PP2A, SUBUNIT B, B-ALPHA ISOFORM) (PP2A, SUBUNIT B, B55-ALPHA ISOFORM) (PP2A, SUBUNIT B, PR55-ALPHA ISOFORM) (PP2A, SUBUNIT B, R2-ALPHA ISOFORM). [SWISSPROT;Acc:Q0" 0.270031751
0.352603 0.0444453 3004 ENDO-BETA-N-ACETYLGLUCOSAMINIDASE. [RefSeq;Acc:NM_022759] 0.126049126
0.355321 0.086609 1431 ENTHOPROTIN; EPSIN 4; CLATHRIN INTERACTING PROTEIN LOCALIZED IN THE TRANS-GOLGI REGION. [RefSeq;Acc:NM_014666] 0.24374861
0.35711 0.0828779 1913 HISTONE H4. [SWISSPROT;Acc:P02304] 0.232079471
0.363797 0.0861167 1751 VACUOLAR ATP SYNTHASE SUBUNIT G 2 (EC 3.6.3.14) (V-ATPASE G SUBUNIT 2) (VACUOLAR PROTON PUMP G SUBUNIT 2) (V-ATPASE 13 KDA SUBUNIT 2). [SWISSPROT;Acc:O95670] 0.236716356
0.364571 0.0840355 2021 "LON PROTEASE HOMOLOG, MITOCHONDRIAL PRECURSOR (EC 3.4.21.-) (LON PROTEASE-LIKE PROTEIN) (LONP) (LONHS). [SWISSPROT;Acc:P36776]" 0.230505169
0.365399 0.0927584 1019 INTERSECTIN 1 (SH3 DOMAIN-CONTAINING PROTEIN 1A) (SH3P17). [SWISSPROT;Acc:Q15811] 0.253855101
0.366045 0.0801834 2401 WILLIAMS-BEUREN SYNDROME CRITICAL REGION PROTEIN 20 COPY B. [RefSeq;Acc:NM_145645] 0.219053395
0.366305 0.0391008 3042 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-7 SUBUNIT. [SWISSPROT;Acc:O60262] 0.106743834
0.381544 0.0798317 2670 TRANSCRIPTION FACTOR MAFG (V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG G) (HMAF). [SWISSPROT;Acc:O15525] 0.209233273

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/