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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Hugo Rank final description expected Gene measured
Results: HTML CSV LaTeX Showing element 401 to 450 of 3206 in total
Hugo
Rank
final
description
expected
measured
ADAMTS9 1819 0.234266842 ADAMTS-9 PRECURSOR (EC 3.4.24.-) (A DISINTEGRIN AND METALLOPROTEINASE WITH THROMBOSPONDIN MOTIFS 9) (ADAM-TS 9) (ADAM-TS9). [SWISSPROT;Acc:Q9P2N4] 0.326867 0.0765741
ADC 2505 0.214784073 ORNITHINE DECARBOXYLASE-LIKE PROTEIN (EC 4.1.1.17) (ODC-PARALOGUE) (ODC-P). [SWISSPROT;Acc:Q96A70] 0.827431 0.177719
ADCK1 1651 0.238973393 AARF DOMAIN CONTAINING KINASE 1. [RefSeq;Acc:NM_020421] 0.142333 0.0340138
ADCK2 1652 AARF DOMAIN CONTAINING KINASE 2; PUTATIVE UBIQUINONE BIOSYNTHESIS PROTEIN AARF. [RefSeq;Acc:NM_052853]
ADCK4 1653 0.238973088 AARF DOMAIN CONTAINING KINASE 4. [RefSeq;Acc:NM_024876] 0.115005 0.0274831
ADCY5 844 0.260704466 "ADENYLATE CYCLASE, TYPE V (EC 4.6.1.1) (ATP PYROPHOSPHATE-LYASE) (ADENYLYL CYCLASE) (FRAGMENT). [SWISSPROT;Acc:O95622]" 0.625183 0.162988
ADCY6 845 0.260704379 "ADENYLATE CYCLASE, TYPE VI (EC 4.6.1.1) (ATP PYROPHOSPHATE-LYASE) (CA(2+)-INHIBITABLE ADENYLYL CYCLASE). [SWISSPROT;Acc:O43306]" 0.761721 0.198584
ADD1 1460 0.243062862 ALPHA ADDUCIN (ERYTHROCYTE ADDUCIN ALPHA SUBUNIT). [SWISSPROT;Acc:P35611] 0.753661 0.183187
ADD2 1459 0.243102741 BETA ADDUCIN (ERYTHROCYTE ADDUCIN BETA SUBUNIT). [SWISSPROT;Acc:P35612] 0.672876 0.163578
ADD3 1456 0.243138464 GAMMA ADDUCIN (ADDUCIN-LIKE PROTEIN 70). [SWISSPROT;Acc:Q9UEY8] 0.755771 0.183757
ADI1 2430 0.217496151 SIPL PROTEIN. [RefSeq;Acc:NM_018269] 0.429323 0.0933761
ADIPOR2 7 0.589835975 ADIPONECTIN RECEPTOR 2. [RefSeq;Acc:NM_024551] 0.428531 0.252763
ADK 2171 0.227023634 ADENOSINE KINASE (EC 2.7.1.20) (AK) (ADENOSINE 5'-PHOSPHOTRANSFERASE). [SWISSPROT;Acc:P55263] 0.691417 0.156968
ADRM1 1125 0.250678078 ADHESION REGULATING MOLECULE 1 PRECURSOR (110 KDA CELL MEMBRANE GLYCOPROTEIN) (GP110). [SWISSPROT;Acc:Q16186] 0.464548 0.116452
ADSL 933 0.256823546 ADENYLOSUCCINATE LYASE (EC 4.3.2.2) (ADENYLOSUCCINASE) (ASL) (ASASE). [SWISSPROT;Acc:P30566] 1.12698 0.289435
ADSS 2179 0.226800926 ADENYLOSUCCINATE SYNTHETASE (EC 6.3.4.4) (IMP--ASPARTATE LIGASE) (ADSS) (AMPSASE). [SWISSPROT;Acc:P30520] 1.47327 0.334139
ADSSL1 2178 0.226885583 ADENYLOSUCCINATE SYNTHASE-LIKE 1. [RefSeq;Acc:NM_152328] 1.7008 0.385887
AFG3L2 993 0.255052025 AFG3-LIKE PROTEIN 2 (EC 3.4.24.-) (PARAPLEGIN-LIKE PROTEIN). [SWISSPROT;Acc:Q9Y4W6] 1.10619 0.282136
AGGF1 1120 0.250798974 1.1302 0.283453
AGPAT2 2873 0.18883127 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE BETA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 2) (1-AGPAT 2) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-BETA) (LPAAT-BETA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 2). [SWISSPROT;Acc:O15120] 1.05097 0.198456
AGPAT3 2855 0.190925302 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE GAMMA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 3) (1-AGPAT 3) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-GAMMA) (LPAAT-GAMMA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 3). [SWISSPROT;Acc:Q9NRZ7] 1.12158 0.214138
AGPAT4 2854 0.191089509 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE DELTA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 4) (1-AGPAT 4) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-DELTA) (LPAAT-DELTA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 4). [SWISSPROT;Acc:Q9NRZ5] 1.26323 0.24139
AGXT 2351 0.220382822 SERINE--PYRUVATE AMINOTRANSFERASE (EC 2.6.1.51) (SPT) (ALANINE-- GLYOXYLATE AMINOTRANSFERASE) (EC 2.6.1.44) (AGT). [SWISSPROT;Acc:P21549] 0.651843 0.143655
AHCY 2335 0.221186589 ADENOSYLHOMOCYSTEINASE (EC 3.3.1.1) (S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE) (ADOHCYASE). [SWISSPROT;Acc:P23526] 0.605534 0.133936
AHCYL1 54 0.411155303 PUTATIVE ADENOSYLHOMOCYSTEINASE 2 (EC 3.3.1.1) (S-ADENOSYL-L- HOMOCYSTEINE HYDROLASE) (ADOHCYASE). [SWISSPROT;Acc:O43865] 0.629835 0.25896
AIFM1 2697 0.207985545 "PROGRAMMED CELL DEATH PROTEIN 8, MITOCHONDRIAL PRECURSOR (EC 1.-.-.-) (APOPTOSIS-INDUCING FACTOR). [SWISSPROT;Acc:O95831]" 0.5396 0.112229
AIFM2 2232 0.224215966 APOPTOSIS-INDUCING FACTOR (AIF)-HOMOLOGOUS MITOCHONDRION-ASSOCIATED INDUCER OF DEATH; P53-RESPONSIVE GENE 3. [RefSeq;Acc:NM_032797] 1.15907 0.259882
AIFM3 2693 0.208211209 0.586832 0.122185
AIG1 208 0.320555328 ANDROGEN-INDUCED 1; CGI-103 PROTEIN; ANDROGEN INDUCED PROTEIN. [RefSeq;Acc:NM_016108] 0.87768 0.281345
AIP 2048 0.229948436 AH RECEPTOR-INTERACTING PROTEIN (AIP) (IMMUNOPHILIN HOMOLOG ARA9) (HBV-X ASSOCIATED PROTEIN 2). [SWISSPROT;Acc:O00170] 0.226516 0.052087
AIPL1 2050 0.22994768 ARYL-HYDROCARBON INTERACTING PROTEIN-LIKE 1. [SWISSPROT;Acc:Q9NZN9] 0.178518 0.0410498
AK2 1912 0.232097856 "ADENYLATE KINASE ISOENZYME 2, MITOCHONDRIAL (EC 2.7.4.3) (ATP-AMP TRANSPHOSPHORYLASE). [SWISSPROT;Acc:P54819]" 1.87377 0.434898
AK3 1962 0.231218051 GTP:AMP PHOSPHOTRANSFERASE MITOCHONDRIAL (EC 2.7.4.10) (AK3) (ADENYLATE KINASE 3 ALPHA LIKE 1). [SWISSPROT;Acc:Q9UIJ7] 1.82907 0.422914
AKR7A2 945 0.256405843 AFLATOXIN B1 ALDEHYDE REDUCTASE 1 (EC 1.-.-.-) (AFB1-AR 1) (ALDOKETOREDUCTASE 7). [SWISSPROT;Acc:O43488] 0.242271 0.0621197
AKR7A3 943 0.256406128 AFLATOXIN B1 ALDEHYDE REDUCTASE 2 (EC 1.-.-.-) (AFB1-AR 2). [SWISSPROT;Acc:O95154] 0.251556 0.0645005
AKT1 1438 0.24352642 RAC-ALPHA SERINE/THREONINE KINASE (EC 2.7.1.-) (RAC-PK-ALPHA) (PROTEIN KINASE B) (PKB) (C-AKT). [SWISSPROT;Acc:P31749] 0.089649 0.0218319
AKT2 1437 0.24352643 "RAC-BETA SERINE/THREONINE PROTEIN KINASE (EC 2.7.1.-) (RAC-PK-BETA) (PROTEIN KINASE AKT-2) (PROTEIN KINASE B, BETA) (PKB BETA). [SWISSPROT;Acc:P31751]" 0.0870115 0.0211896
AKT3 1440 0.243525633 "RAC-GAMMA SERINE/THREONINE PROTEIN KINASE (EC 2.7.1.-) (RAC-PK-GAMMA) (PROTEIN KINASE AKT-3) (PROTEIN KINASE B, GAMMA) (PKB GAMMA) (STK-2). [SWISSPROT;Acc:Q9Y243]" 0.102427 0.0249436
AKTIP 494 0.274302663 FUSED TOES HOMOLOG; LIKELY ORTHOLOG OF MOUSE FUSED TOES. [RefSeq;Acc:NM_022476] 1.01314 0.277907
ALAD 1299 0.245824013 DELTA-AMINOLEVULINIC ACID DEHYDRATASE (EC 4.2.1.24) (PORPHOBILINOGEN SYNTHASE) (ALADH). [SWISSPROT;Acc:P13716] 0.627636 0.154288
ALAS1 2596 0.212890596 "5-AMINOLEVULINIC ACID SYNTHASE, NONSPECIFIC, MITOCHONDRIAL PRECURSOR (EC 2.3.1.37) (DELTA-AMINOLEVULINATE SYNTHASE) (DELTA-ALA SYNTHETASE) (ALAS-H). [SWISSPROT;Acc:P13196]" 0.297814 0.0634018
ALAS2 2599 0.212890431 "5-AMINOLEVULINIC ACID SYNTHASE, ERYTHROID-SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 2.3.1.37) (DELTA-AMINOLEVULINATE SYNTHASE) (DELTA-ALA SYNTHETASE) (ALAS-E). [SWISSPROT;Acc:P22557]" 0.360019 0.0766446
ALDH18A1 1681 0.238166751 DELTA 1-PYRROLINE-5-CARBOXYLATE SYNTHETASE (P5CS) [INCLUDES: GLUTAMATE 5-KINASE (EC 2.7.2.11) (GAMMA-GLUTAMYL KINASE) (GK); GAMMA-GLUTAMYL PHOSPHATE REDUCTASE (GPR) (EC 1.2.1.41) (GLUTAMATE-5-SEMIALDEHYDE DEHYDROGENASE) (GLUTAMYL-GAMMA-SEMIALDEHYDE DEHYDR 0.0944225 0.0224883
ALDH6A1 940 0.256406657 "METHYLMALONATE-SEMIALDEHYDE DEHYDROGENASE [ACYLATING], MITOCHONDRIAL PRECURSOR (EC 1.2.1.27) (MMSDH). [SWISSPROT;Acc:Q02252]" 0.248593 0.0637409
ALG1 3126 0.073608415 "BETA-1,4 MANNOSYLTRANSFERASE. [RefSeq;Acc:NM_019109]" 0.785148 0.0577935
AMMECR1 2177 0.226939375 AMMECR1 PROTEIN. [RefSeq;Acc:NM_015365] 0.154573 0.0350787
AMOT 1214 0.24805925 ANGIOMOTIN. [RefSeq;Acc:NM_133265] 0.323509 0.0802494
AMOTL2 1211 0.248059294 ANGIOMOTIN LIKE 2; LEMAN COILED-COIL PROTEIN; ANGIOMOTIN-LIKE PROTEIN 2. [RefSeq;Acc:NM_016201] 0.259184 0.064293
AMPD2 2986 0.138195 AMP DEAMINASE 2 (EC 3.5.4.6) (AMP DEAMINASE ISOFORM L). [SWISSPROT;Acc:Q01433] 1 0.138195
AMT 2071 0.229446017 "AMINOMETHYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.2.10) (GLYCINE CLEAVAGE SYSTEM T PROTEIN) (GCVT). [SWISSPROT;Acc:P48728]" 0.569999 0.130784

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/