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

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/