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

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/