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 Hugo expected Gene final Rank description
Results: HTML CSV LaTeX Showing element 951 to 1000 of 3206 in total
measured
Hugo
expected
final
Rank
description
0.0621046 UTRN 0.250362 0.24805921 1217 UTROPHIN (DYSTROPHIN-RELATED PROTEIN 1) (DRP1) (DRP). [SWISSPROT;Acc:P46939]
0.0621197 AKR7A2 0.242271 0.256405843 945 AFLATOXIN B1 ALDEHYDE REDUCTASE 1 (EC 1.-.-.-) (AFB1-AR 1) (ALDOKETOREDUCTASE 7). [SWISSPROT;Acc:O43488]
0.0621484 TSNARE1 0.224949 0.276277734 449
0.0621814 DAD1 0.272579 0.228122489 2122 DEFENDER AGAINST CELL DEATH 1 (DAD-1). [SWISSPROT;Acc:P46966]
0.0623579 ACADM 0.311942 0.199902225 2794 "ACYL-COA DEHYDROGENASE, MEDIUM-CHAIN SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 1.3.99.3) (MCAD). [SWISSPROT;Acc:P11310]"
STIM1 2793 STROMAL INTERACTION MOLECULE 1 PRECURSOR. [SWISSPROT;Acc:Q13586]
0.0624093 DDI1 0.2611 0.239024512 1643
0.0627928 FMO5 0.269788 0.232748677 1885 DIMETHYLANILINE MONOOXYGENASE [N-OXIDE FORMING] 5 (EC 1.14.13.8) (HEPATIC FLAVIN-CONTAINING MONOOXYGENASE 5) (FMO 5) (DIMETHYLANILINE OXIDASE 5). [SWISSPROT;Acc:P49326]
FMO6P 1884 PUTATIVE DIMETHYLANILINE MONOOXYGENASE [N-OXIDE FORMING] 6 (EC 1.14.13.8) (FLAVIN-CONTAINING MONOOXYGENASE 6) (FMO 6) (DIMETHYLANILINE OXIDASE 6). [SWISSPROT;Acc:O60774]
0.0628075 SGCZ 0.269823 0.232772966 1876 SARCOGLYCAN ZETA; ZETA-SARCOGLYCAN. [RefSeq;Acc:NM_139167]
0.0628846 TMBIM1 0.276631 0.22732304 2152 PP1201 PROTEIN. [RefSeq;Acc:NM_022152]
0.0629265 BSCL2 0.276021 0.227977219 2136
0.062927 RHAG 0.295267 0.213118974 2583 RHESUS BLOOD GROUP-ASSOCIATED GLYCOPROTEIN (ERYTHROCYTE PLASMA MEMBRANE 50 KDA GLYCOPROTEIN) (RH50A). [SWISSPROT;Acc:Q02094]
0.063055 ATP6V1G1 0.266374 0.236716046 1756 VACUOLAR ATP SYNTHASE SUBUNIT G 1 (EC 3.6.3.14) (V-ATPASE G SUBUNIT 1) (VACUOLAR PROTON PUMP G SUBUNIT 1) (V-ATPASE 13 KDA SUBUNIT 1) (VACUOLAR ATP SYNTHASE SUBUNIT M16). [SWISSPROT;Acc:O75348]
0.0630725 SGCD 0.270962 0.232772492 1878 DELTA-SARCOGLYCAN (SG-DELTA) (35 KDA DYSTROPHIN-ASSOCIATED GLYCOPROTEIN) (35DAG). [SWISSPROT;Acc:Q92629]
0.06311 HDAC9 0.29571 0.213418552 2570 HISTONE DEACETYLASE 9 (HD9) (HD7B) (HD7). [SWISSPROT;Acc:Q9UKV0]
0.0634018 ALAS1 0.297814 0.212890596 2596 "5-AMINOLEVULINIC ACID SYNTHASE, NONSPECIFIC, MITOCHONDRIAL PRECURSOR (EC 2.3.1.37) (DELTA-AMINOLEVULINATE SYNTHASE) (DELTA-ALA SYNTHETASE) (ALAS-H). [SWISSPROT;Acc:P13196]"
0.063502 ATP1A1 0.250657 0.253342217 1032 SODIUM/POTASSIUM-TRANSPORTING ATPASE ALPHA-1 CHAIN PRECURSOR (EC 3.6.3.9) (SODIUM PUMP 1) (NA+/K+ ATPASE 1). [SWISSPROT;Acc:P05023]
ATP1A2 1031 SODIUM/POTASSIUM-TRANSPORTING ATPASE ALPHA-2 CHAIN PRECURSOR (EC 3.6.3.9) (SODIUM PUMP 2) (NA+/K+ ATPASE 2). [SWISSPROT;Acc:P50993]
0.0635814 HMGCS2 0.299985 0.211948597 2605 "HYDROXYMETHYLGLUTARYL-COA SYNTHASE, MITOCHONDRIAL PRECURSOR (EC 2.3.3.10) (HMG-COA SYNTHASE) (3-HYDROXY-3-METHYLGLUTARYL COENZYME A SYNTHASE). [SWISSPROT;Acc:P54868]"
0.0637011 no value 0.29203 0.218132041 2423 TRANSCRIPTION ELONGATION FACTOR A PROTEIN 1 (TRANSCRIPTION ELONGATION FACTOR S-II PROTEIN 1) (TRANSCRIPTION ELONGATION FACTOR TFIIS.O). [SWISSPROT;Acc:P23193]
0.063706 TCP1 0.673766 0.094552115 3099 "T-COMPLEX PROTEIN 1, ALPHA SUBUNIT (TCP-1-ALPHA) (CCT-ALPHA). [SWISSPROT;Acc:P17987]"
0.0637106 ABLIM3 0.156874 0.406125935 77
0.0637349 no value 0.231274 0.27558177699999997 460 COLLAGEN ALPHA 5(IV) CHAIN PRECURSOR. [SWISSPROT;Acc:P29400]
0.0637409 ALDH6A1 0.248593 0.256406657 940 "METHYLMALONATE-SEMIALDEHYDE DEHYDROGENASE [ACYLATING], MITOCHONDRIAL PRECURSOR (EC 1.2.1.27) (MMSDH). [SWISSPROT;Acc:Q02252]"
0.0637963 PRDX5 0.274826 0.232133423 1910 "PEROXIREDOXIN 5, MITOCHONDRIAL PRECURSOR (PRX-V) (PEROXISOMAL ANTIOXIDANT ENZYME) (PLP) (THIOREDOXIN PEROXIDASE PMP20) (ANTIOXIDANT ENZYME B166) (AOEB166) (TPX TYPE VI) (LIVER TISSUE 2D-PAGE SPOT 71B) (ALU CO-REPRESSOR 1) (SBBI10). [SWISSPROT;Acc:P"
0.06383 no value 0.157168 0.406125929 78 ASPARTATE BETA-HYDROXYLASE ISOFORM B; JUNCTIN ISOFORM 1; JUNCTATE; ASPARTYL/ASPARAGINYL-BETA-HYDROXYLASE; PEPTIDE-ASPARTATE BETA-DIOXYGENASE; HUMBUG. [RefSeq;Acc:NM_032468]
0.0640044 PIH1D2 0.290417 0.220387925 2349
0.0640341 no value 0.280704 0.228119656 2127 "GLYCINE DEHYDROGENASE [DECARBOXYLATING], MITOCHONDRIAL PRECURSOR (EC 1.4.4.2) (GLYCINE DECARBOXYLASE) (GLYCINE CLEAVAGE SYSTEM P- PROTEIN). [SWISSPROT;Acc:P23378]"
0.0640593 SNTA1 0.258242 0.248059185 1218 "ALPHA-1-SYNTROPHIN (59 KDA DYSTROPHIN-ASSOCIATED PROTEIN A1, ACIDIC COMPONENT 1) (PRO-TGF-ALPHA CYTOPLASMIC DOMAIN-INTERACTING PROTEIN 1) (TACIP1) (SYNTROPHIN 1). [SWISSPROT;Acc:Q13424]"
0.0641829 CLSTN3 0.33238 0.193100969 2831 CALSYNTENIN-3 PRECURSOR. [SWISSPROT;Acc:Q9BQT9]
0.0641898 MARS 0.297931 0.2154519 2494 METHIONYL-TRNA SYNTHETASE (EC 6.1.1.10) (METHIONINE--TRNA LIGASE) (METRS). [SWISSPROT;Acc:P56192]
0.0642768 HDAC4 0.301176 0.213419396 2569 HISTONE DEACETYLASE 4 (HD4). [SWISSPROT;Acc:P56524]
0.064293 AMOTL2 0.259184 0.248059294 1211 ANGIOMOTIN LIKE 2; LEMAN COILED-COIL PROTEIN; ANGIOMOTIN-LIKE PROTEIN 2. [RefSeq;Acc:NM_016201]
0.0643408 MAGEA4 0.98408 0.065381676 3146 MELANOMA-ASSOCIATED ANTIGEN 12 (MAGE-12 ANTIGEN) (MAGE12F). [SWISSPROT;Acc:P43365]
0.064364 GARS 0.264372 0.243459973 1447 GLYCYL-TRNA SYNTHETASE (EC 6.1.1.14) (GLYCINE--TRNA LIGASE) (GLYRS). [SWISSPROT;Acc:P41250]
0.0644285 SIPA1L3 0.242538 0.26564291 692
0.0645005 AKR7A3 0.251556 0.256406128 943 AFLATOXIN B1 ALDEHYDE REDUCTASE 2 (EC 1.-.-.-) (AFB1-AR 2). [SWISSPROT;Acc:O95154]
0.0645342 HSPE1 0.251688 0.25640555 951 "10 KDA HEAT SHOCK PROTEIN, MITOCHONDRIAL (HSP10) (10 KDA CHAPERONIN) (CPN10). [SWISSPROT;Acc:Q04984]"
KCNAB1 950 VOLTAGE-GATED POTASSIUM CHANNEL BETA-1 SUBUNIT (K+ CHANNEL BETA-1 SUBUNIT) (KV-BETA-1). [SWISSPROT;Acc:Q14722]
0.0645881 MAGEE2 0.987862 0.065381703 3143 HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN HCA3. [RefSeq;Acc:NM_138703]
0.0646293 no value 0.988493 0.065381647 3148 MELANOMA-ASSOCIATED ANTIGEN 3 (MAGE-3 ANTIGEN) (ANTIGEN MZ2-D). [SWISSPROT;Acc:P43357]
0.0646597 COL4A3BP 0.280961 0.230137635 2042 GOODPASTURE ANTIGEN-BINDING PROTEIN (EC 2.7.1.37) (GPBP) (COLLAGEN TYPE IV ALPHA 3 BINDING PROTEIN) (STAR-RELATED LIPID TRANSFER PROTEIN 11) (STARD11) (START DOMAIN-CONTAINING PROTEIN 11). [SWISSPROT;Acc:Q9Y5P4]
0.0646696 RHBG 0.303444 0.21311873 2584 "RHESUS BLOOD GROUP, B GLYCOPROTEIN; RH TYPE B GLYCOPROTEIN. [RefSeq;Acc:NM_020407]"
0.0646859 HEY1 0.159275 0.406127139 68 HAIRY/ENHANCER-OF-SPLIT RELATED WITH YRPW MOTIF 1 (HAIRY AND ENHANCER OF SPLIT RELATED-1) (HESR-1) (CARDIOVASCULAR HELIX-LOOP-HELIX FACTOR 2) (HES-RELATED REPRESSOR PROTEIN 2 HERP2). [SWISSPROT;Acc:Q9Y5J3]
0.0646874 API5 0.27327 0.236716068 1755 APOPTOSIS INHIBITOR 5; FIBROBLAST GROWTH FACTOR 2-INTERACTING FACTOR 2; API5-LIKE 1. [RefSeq;Acc:NM_006595]
0.0647324 MAGEA2B 0.990069 0.065381706 3142 MELANOMA-ASSOCIATED ANTIGEN 2 (MAGE-2 ANTIGEN). [SWISSPROT;Acc:P43356]
0.0647928 TNPO3 0.289906 0.223495892 2247 TRANSPORTIN-SR; IMPORTIN 12. [RefSeq;Acc:NM_012470]
0.0648148 no value 0.99133 0.065381659 3147 MELANOMA-ASSOCIATED ANTIGEN 1 (MAGE-1 ANTIGEN) (ANTIGEN MZ2-E). [SWISSPROT;Acc:P43355]
0.0648248 GYG1 0.285541 0.22702449 2169 GLYCOGENIN-1 (EC 2.4.1.186). [SWISSPROT;Acc:P46976]

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/