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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expected Gene Rank measured Hugo description final
Results: HTML CSV LaTeX Showing element 1852 to 1901 of 3206 in total
expected
Rank
measured
Hugo
description
final
0.66831 1708 0.15883 NSF VESICLE-FUSING ATPASE (EC 3.6.4.6) (VESICULAR-FUSION PROTEIN NSF) (N- ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN) (NEM-SENSITIVE FUSION PROTEIN). [SWISSPROT;Acc:P46459] 0.23765917
0.66836 505 0.183159 IMPDH1 INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 1 (EC 1.1.1.205) (IMP DEHYDROGENASE 1) (IMPDH-I) (IMPD 1). [SWISSPROT;Acc:P20839] 0.274042432
0.669424 2419 0.146069 GCN5L2 GENERAL CONTROL OF AMINO ACID SYNTHESIS PROTEIN 5-LIKE 2 (EC 2.3.1.-) (HISTONE ACETYLTRANSFERASE GCN5) (HSGCN5). [SWISSPROT;Acc:Q92830] 0.218201021
0.670248 2426 0.146042 G6PD GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE (EC 1.1.1.49) (G6PD). [SWISSPROT;Acc:P11413] 0.217892482
0.671325 2265 0.149637 SBDS SHWACHMAN-BODIAN-DIAMOND SYNDROME PROTEIN (CGI-97). [SWISSPROT;Acc:Q9Y3A5] 0.222898
0.671355 704 0.178008 WASF3 WISKOTT-ALDRICH SYNDROME PROTEIN FAMILY MEMBER 3 (WASP-FAMILY PROTEIN MEMBER 3) (VERPROLIN HOMOLOGY DOMAIN-CONTAINING PROTEIN 3). [SWISSPROT;Acc:Q9UPY6] 0.265147351
0.671805 573 0.181797 PPP2R1B "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 65 KDA REGULATORY SUBUNIT A, BETA ISOFORM (PP2A, SUBUNIT A, PR65-BETA ISOFORM) (PP2A, SUBUNIT A, R1-BETA ISOFORM). [SWISSPROT;Acc:P30154]" 0.270609775
0.672152 2428 0.146403 PLD2 PHOSPHOLIPASE D2 (EC 3.1.4.4) (PLD 2) (CHOLINE PHOSPHATASE 2) (PHOSPHATIDYLCHOLINE-HYDROLYZING PHOSPHOLIPASE D2) (PLD1C) (HPLD2). [SWISSPROT;Acc:O14939] 0.21781234
0.672496 300 0.201663 CAPN2 "CALPAIN 2, LARGE [CATALYTIC] SUBUNIT PRECURSOR (EC 3.4.22.17) (CALCIUM-ACTIVATED NEUTRAL PROTEINASE) (CANP) (M-TYPE) (M-CALPAIN) (MILLIMOLAR-CALPAIN) (CALPAIN LARGE POLYPEPTIDE L2). [SWISSPROT;Acc:P17655]" 0.299872416
0.672842 1683 0.160247 no value NUCLEOLAR PROTEIN NOP5 (NUCLEOLAR PROTEIN 5) (NOP58) (HSPC120). [SWISSPROT;Acc:Q9Y2X3] 0.238164383
0.672876 1459 0.163578 ADD2 BETA ADDUCIN (ERYTHROCYTE ADDUCIN BETA SUBUNIT). [SWISSPROT;Acc:P35612] 0.243102741
0.673766 3099 0.063706 TCP1 "T-COMPLEX PROTEIN 1, ALPHA SUBUNIT (TCP-1-ALPHA) (CCT-ALPHA). [SWISSPROT;Acc:P17987]" 0.094552115
0.673879 1127 0.168913 OXA1L "CYTOCHROME OXIDASE BIOGENESIS PROTEIN OXA1, MITOCHONDRIAL PRECURSOR (OXA1-LIKE PROTEIN) (OXA1HS). [SWISSPROT;Acc:Q15070]" 0.250657759
1128 MRPL34 "60S RIBOSOMAL PROTEIN L34, MITOCHONDRIAL PRECURSOR (L34MT). [SWISSPROT;Acc:Q9BQ48]"
0.67395 1598 0.161804 PPP4C SERINE/THREONINE PROTEIN PHOSPHATASE 4 (EC 3.1.3.16) (PP4) (PROTEIN PHOSPHATASE X) (PP-X). [SWISSPROT;Acc:P33172] 0.240083092
0.674093 2061 0.1548 GPD1 "GLYCEROL-3-PHOSPHATE DEHYDROGENASE [NAD+], CYTOPLASMIC (EC 1.1.1.8) (GPD-C) (GPDH-C). [SWISSPROT;Acc:P21695]" 0.229641904
0.674746 1344 0.165502 RAB3IP RAB3A INTERACTING PROTEIN ISOFORM ALPHA 1; RABIN3; SSX2 INTERACTING PROTEIN. [RefSeq;Acc:NM_022456] 0.245280446
0.675264 217 0.215654 DRAP1 DR1-ASSOCIATED PROTEIN 1; NEGATIVE COFACTOR 2 ALPHA; DR1-ASSOCIATED COREPRESSOR. [RefSeq;Acc:NM_006442] 0.319362501
0.675823 253 0.210781 DIRAS2 DI-RAS2. [RefSeq;Acc:NM_017594] 0.311887876
0.678587 861 0.176631 PEO1 TWINKLE; LIKELY ORTHOLOG OF MOUSE T7 GP4-LIKE PROTEIN WITH INTRAMITOCHONDRIAL NUCLEOID LOCALIZATION. [RefSeq;Acc:NM_021830] 0.260292343
0.679075 2617 0.143053 MAP2K6 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 6 (EC 2.7.1.-) (MAP KINASE KINASE 6) (MAPKK 6) (MAPK/ERK KINASE 6) (SAPKK3). [SWISSPROT;Acc:P52564] 0.210658617
0.679841 1328 0.166892 no value NIF3-LIKE PROTEIN 1 (AMYOTROPHIC LATERAL SCLEROSIS 2 CHROMOSOMAL REGION CANDIDATE GENE PROTEIN 1) (MY018 PROTEIN) (MDS015). [SWISSPROT;Acc:Q9GZT8] 0.245486812
0.679961 2945 0.103715 SLC30A9 0.152530807
0.680239 774 0.179057 TOM1L2 TARGET OF MYB1-LIKE 2; TARGET OF MYB1 (CHICKEN) HOMOLOG-LIKE 2. [RefSeq;Acc:NM_144678] 0.263226601
0.681143 947 0.174649 YIPF5 GOLGI MEMBRANE PROTEIN SB140; SMOOTH MUSCLE CELL ASSOCIATED PROTEIN 5. [RefSeq;Acc:NM_030799] 0.256405777
0.682084 2938 0.107134 VPS37B 0.157068631
0.682179 1 0.790808 UFC1 PROTEIN CGI-126 (PROTEIN HSPC155). [SWISSPROT;Acc:Q9Y3C8] 1.159238264
0.682226 2146 0.155283 MMS19 "MMS19-LIKE (MET18 HOMOLOG, S. CEREVISIAE); HOMOLOG OF YEAST MMS19; MMS19 (MET18 S. CEREVISIAE)-LIKE. [RefSeq;Acc:NM_022362]" 0.227612258
0.685711 301 0.205623 CAPN1 "CALPAIN 1, LARGE [CATALYTIC] SUBUNIT (EC 3.4.22.17) (CALCIUM-ACTIVATED NEUTRAL PROTEINASE) (CANP) (MU-TYPE) (MUCANP) (MICROMOLAR-CALPAIN). [SWISSPROT;Acc:P07384]" 0.299868312
0.685844 1778 0.161564 ASS1 ARGININOSUCCINATE SYNTHASE (EC 6.3.4.5) (CITRULLINE--ASPARTATE LIGASE). [SWISSPROT;Acc:P00966] 0.235569605
0.687157 2279 0.152886 GDPD3 0.222490639
0.68743 59 0.28264 DLGAP3 DISKS LARGE-ASSOCIATED PROTEIN 3 (DAP-3) (SAP90/PSD-95-ASSOCIATED PROTEIN 3) (SAPAP3) (PSD-95/SAP90 BINDING PROTEIN 3) (FRAGMENT). [SWISSPROT;Acc:O95886] 0.41115459
0.689453 2958 0.100774 SHOC2 LEUCINE-RICH REPEAT PROTEIN SHOC-2 (RAS-BINDING PROTEIN SUR-8). [SWISSPROT;Acc:Q9UQ13] 0.146165148
2959 FRMPD4
0.691417 2171 0.156968 ADK ADENOSINE KINASE (EC 2.7.1.20) (AK) (ADENOSINE 5'-PHOSPHOTRANSFERASE). [SWISSPROT;Acc:P55263] 0.227023634
0.691419 2235 0.154876 IDH3A "ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT ALPHA, MITOCHONDRIAL PRECURSOR (EC 1.1.1.41) (ISOCITRIC DEHYDROGENASE) (NAD+-SPECIFIC ICDH). [SWISSPROT;Acc:P50213]" 0.223997316
0.693413 1984 0.160147 EPHX1 EPOXIDE HYDROLASE 1 (EC 3.3.2.3) (MICROSOMAL EPOXIDE HYDROLASE) (EPOXIDE HYDRATASE). [SWISSPROT;Acc:P07099] 0.230954712
0.693873 1791 0.163024 POLR3K DNA-DIRECTED RNA POLYMERASES III 12.5 KDA POLYPEPTIDE (EC 2.7.7.6) (RNA POLYMERASE III C11 SUBUNIT) (HSC11P) (HRPC11) (MY010 PROTEIN). [SWISSPROT;Acc:Q9Y2Y1] 0.234947894
0.694099 2361 0.152908 SUFU SUPPRESSOR OF FUSED. [RefSeq;Acc:NM_016169] 0.220297105
0.694888 2208 0.156444 no value 40S RIBOSOMAL PROTEIN S3A. [SWISSPROT;Acc:P49241] 0.225135561
0.695125 801 0.182131 RFXANK DNA-BINDING PROTEIN RFXANK (REGULATORY FACTOR X SUBUNIT B) (RFX-B) (ANKYRIN REPEAT FAMILY A PROTEIN 1). [SWISSPROT;Acc:O14593] 0.262011868
0.697153 303 0.20849 no value HPAII TINY FRAGMENTS LOCUS 9C. [RefSeq;Acc:NM_022727] 0.299059174
0.698382 2710 0.144805 UTP3 DISRUPTER OF SILENCING 10. [RefSeq;Acc:NM_020368] 0.207343546
0.698388 2702 0.145039 FAM82B 0.207676821
0.699345 1631 0.167352 PHLPP 0.2392982
0.702909 1080 0.177185 PARL PRESENILINS ASSOCIATED RHOMBOID-LIKE PROTEIN. [RefSeq;Acc:NM_018622] 0.252073882
0.703125 2155 0.159792 LARS LEUCYL-TRNA SYNTHETASE. [RefSeq;Acc:NM_020117] 0.227259733
0.703261 73 0.285613 HES1 TRANSCRIPTION FACTOR HES-1 (HAIRY AND ENHANCER OF SPLIT 1) (HAIRY- LIKE) (HHL) (HAIRY HOMOLOG). [SWISSPROT;Acc:Q14469] 0.406126602
0.7037 2156 0.159922 LARS2 "PROBABLE LEUCYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.4) (LEUCINE--TRNA LIGASE) (LEURS). [SWISSPROT;Acc:Q15031]" 0.227258775
0.704023 1079 0.177598 SOLH "SMALL OPTIC LOBES HOMOLOG; SMALL OPTIC LOBES, DROSOPHILA, HOMOLOG OF. [RefSeq;Acc:NM_005632]" 0.252261645

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/