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 description measured final Hugo
Results: HTML CSV LaTeX Showing element 802 to 851 of 3206 in total
expected
Rank
description
measured
final
Hugo
0.24054 2130 "RUNT-RELATED TRANSCRIPTION FACTOR 2 (CORE-BINDING FACTOR, ALPHA 1 SUBUNIT) (CBF-ALPHA 1) (ACUTE MYELOID LEUKEMIA 3 PROTEIN) (ONCOGENE AML-3) (POLYOMAVIRUS ENHANCER BINDING PROTEIN 2 ALPHA A SUBUNIT) (PEBP2-ALPHA A) (PEA2-ALPHA A) (SL3-3 ENHANCER FACTOR 1 " 0.0548378 0.227977883 RUNX2
2131 NEUROPILIN- AND TOLLOID-LIKE PROTEIN 2 PRECURSOR. [RefSeq;Acc:NM_018092] NETO2
0.241075 1704 DJ408B20.3 (NOVEL PROTEIN SIMILAR TO 60S ACIDIC RIBOSOMAL PROTEIN P2 (RPLP2)). [SPTREMBL;Acc:Q9H5A9] 0.0573148 0.237746759 no value
0.24133 399 THYROID RECEPTOR INTERACTING PROTEIN 3 (TRIP-3) (FRAGMENT). [SWISSPROT;Acc:Q15649] 0.0671887 0.278410061 ZNHIT3
0.241353 2769 SIMILAR TO ZINC FINGER PROTEIN 277. [SPTREMBL;Acc:Q8WWA6] 0.0486609 0.201617133 no value
0.241467 2911 0.0420495 0.174141808 ANKS6
0.241784 398 NUCLEAR FRAGILE X MENTAL RETARDATION PROTEIN INTERACTING PROTEIN 1; NUCLEAR FRAGILE X MENTAL RETARDATION INTERCATING PROTEIN 1; NUCLEAR FRAGILE X MENTAL RETARDATION PROTEIN-INTERACTING PROTEIN 1. [RefSeq;Acc:NM_012345] 0.0673151 0.278410068 NUFIP1
0.242271 945 AFLATOXIN B1 ALDEHYDE REDUCTASE 1 (EC 1.-.-.-) (AFB1-AR 1) (ALDOKETOREDUCTASE 7). [SWISSPROT;Acc:O43488] 0.0621197 0.256405843 AKR7A2
0.242538 692 0.0644285 0.26564291 SIPA1L3
0.243254 386 "GRPE PROTEIN HOMOLOG 2, MITOCHONDRIAL PRECURSOR (MT-GRPE#2). [SWISSPROT;Acc:Q8TAA5]" 0.0678064 0.278747318 GRPEL2
0.243524 1877 GAMMA-SARCOGLYCAN (GAMMA-SG) (35 KDA DYSTROPHIN-ASSOCIATED GLYCOPROTEIN) (35DAG). [SWISSPROT;Acc:Q13326] 0.0566858 0.232772951 SGCG
0.24397 2797 STROMAL INTERACTION MOLECULE 2 PRECURSOR. [SWISSPROT;Acc:Q9P246] 0.0487701 0.199902037 STIM2
0.24446 110 DNA POLYMERASE EPSILON SUBUNIT B (EC 2.7.7.7) (DNA POLYMERASE II SUBUNIT B). [SWISSPROT;Acc:P56282] 0.0886771 0.362746871 POLE2
0.245251 1594 CENTAURIN BETA 1 (CNT-B1). [SWISSPROT;Acc:Q15027] 0.058923 0.240255901 CENTB1
0.245601 1873 DIMETHYLANILINE MONOOXYGENASE [N-OXIDE FORMING] 3 (EC 1.14.13.8) (HEPATIC FLAVIN-CONTAINING MONOOXYGENASE 3) (FMO 3) (DIMETHYLANILINE OXIDASE 3) (FMO FORM 2) (FMO II). [SWISSPROT;Acc:P31513] 0.0571767 0.232803205 FMO3
0.246217 1171 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 9 (SMAD 9) (MOTHERS AGAINST DPP HOMOLOG 9) (SMAD9) (MADH6). [SWISSPROT;Acc:O15198] 0.0614057 0.24939667 SMAD9
0.247068 1953 60S RIBOSOMAL PROTEIN L14 (CAG-ISL 7). [SWISSPROT;Acc:P50914] 0.0571361 0.231256577 no value
0.247338 1800 0.0580492 0.234695841
1801 MEMBRANE PROTEIN EXPRESSED IN EPITHELIAL-LIKE LUNG ADENOCARCINOMA. [RefSeq;Acc:NM_024792] FAM57A
0.247999 1955 SERINE RACEMASE (EC 5.1.1.-). [SWISSPROT;Acc:Q9GZT4] 0.0573513 0.231256174 SRR
0.248211 191 "T-COMPLEX PROTEIN 1, DELTA SUBUNIT (TCP-1-DELTA) (CCT-DELTA) (STIMULATOR OF TAR RNA BINDING). [SWISSPROT;Acc:P50991]" 0.081012 0.326383601 CCT4
0.248312 1577 SERPIN B12. [SWISSPROT;Acc:Q96P63] 0.0598165 0.240892506 SERPINB12
0.248593 940 "METHYLMALONATE-SEMIALDEHYDE DEHYDROGENASE [ACYLATING], MITOCHONDRIAL PRECURSOR (EC 1.2.1.27) (MMSDH). [SWISSPROT;Acc:Q02252]" 0.0637409 0.256406657 ALDH6A1
0.24878 2219 BETA ENOLASE (EC 4.2.1.11) (2-PHOSPHO-D-GLYCERATE HYDRO-LYASE) (SKELETAL MUSCLE ENOLASE) (MSE) (ENOLASE 3). [SWISSPROT;Acc:P13929] 0.0559551 0.224918 ENO3
0.249916 2276 MANNOSE-P-DOLICHOL UTILIZATION DEFECT 1 PROTEIN (SUPPRESSOR OF LEC15 AND LEC35 GLYCOSYLATION MUTATION HOMOLOG) (SL15). [SWISSPROT;Acc:O75352] 0.0556491 0.222671218 MPDU1
0.250194 852 KINESIN-LIKE PROTEIN KIF13B (KINESIN-LIKE PROTEIN GAKIN). [SWISSPROT;Acc:Q9NQT8] 0.0651843 0.260535025 no value
0.250362 1217 UTROPHIN (DYSTROPHIN-RELATED PROTEIN 1) (DRP1) (DRP). [SWISSPROT;Acc:P46939] 0.0621046 0.24805921 UTRN
0.250657 1031 SODIUM/POTASSIUM-TRANSPORTING ATPASE ALPHA-2 CHAIN PRECURSOR (EC 3.6.3.9) (SODIUM PUMP 2) (NA+/K+ ATPASE 2). [SWISSPROT;Acc:P50993] 0.063502 0.253342217 ATP1A2
1032 SODIUM/POTASSIUM-TRANSPORTING ATPASE ALPHA-1 CHAIN PRECURSOR (EC 3.6.3.9) (SODIUM PUMP 1) (NA+/K+ ATPASE 1). [SWISSPROT;Acc:P05023] ATP1A1
0.250658 2222 0.0563344 0.224746068 MSRB2
0.250685 2151 STEROL REGULATORY ELEMENT BINDING PROTEIN-2 (SREBP-2) (STEROL REGULATORY ELEMENT-BINDING TRANSCRIPTION FACTOR 2). [SWISSPROT;Acc:Q12772] 0.0569865 0.227323135 no value
0.250928 2184 SERINE/THREONINE-PROTEIN KINASE PAK 1 (EC 2.7.1.-) (P21-ACTIVATED KINASE 1) (PAK-1) (P65-PAK) (ALPHA-PAK). [SWISSPROT;Acc:Q13153] 0.0568471 0.226547456 PAK1
2185 CONSERVED OLIGOMERIC GOLGI COMPLEX SUBUNIT 5 (13S GOLGI TRANSPORT COMPLEX 90 KDA SUBUNIT) (GTC-90) (GOLGI TRANSPORT COMPLEX 1). [SWISSPROT;Acc:Q9UP83] COG5
0.250939 2626 MITOGEN-ACTIVATED PROTEIN KINASE-ACTIVATED PROTEIN KINASE 3; MAPKAP KINASE 3. [RefSeq;Acc:NM_004635] 0.052697 0.209999243 MAPKAPK3
0.251275 2258 PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY BETA SUBUNIT (PI3-KINASE P85-BETA SUBUNIT) (PTDINS-3-KINASE P85-BETA). [SWISSPROT;Acc:O00459] 0.0560483 0.223055616 PIK3R2
0.251434 2234 0.0563373 0.224063969 SPATA20
0.251543 1476 DNA REPLICATION LICENSING FACTOR MCM5 (CDC46 HOMOLOG) (P1-CDC46). [SWISSPROT;Acc:P33992] 0.0611188 0.242975555 MCM5
0.251556 943 AFLATOXIN B1 ALDEHYDE REDUCTASE 2 (EC 1.-.-.-) (AFB1-AR 2). [SWISSPROT;Acc:O95154] 0.0645005 0.256406128 AKR7A3
0.251688 950 VOLTAGE-GATED POTASSIUM CHANNEL BETA-1 SUBUNIT (K+ CHANNEL BETA-1 SUBUNIT) (KV-BETA-1). [SWISSPROT;Acc:Q14722] 0.0645342 0.25640555 KCNAB1
951 "10 KDA HEAT SHOCK PROTEIN, MITOCHONDRIAL (HSP10) (10 KDA CHAPERONIN) (CPN10). [SWISSPROT;Acc:Q04984]" HSPE1
0.252363 1593 CENTAURIN BETA 5 (CNT-B5). [SWISSPROT;Acc:Q96P50] 0.0606318 0.240256297 CENTB5
0.252671 690 RIBOSOMAL PROTEIN S6 KINASE ALPHA 6 (EC 2.7.1.37) (S6K-ALPHA 6) (90 KDA RIBOSOMAL PROTEIN S6 KINASE 6) (P90-RSK 6) (RIBOSOMAL S6 KINASE 4) (RSK-4) (PP90RSK4). [SWISSPROT;Acc:Q9UK32] 0.0671204 0.265643465 RPS6KA6
0.25292 688 SIGNAL-INDUCED PROLIFERATION-ASSOCIATED 1-LIKE 1. [RefSeq;Acc:NM_015556] 0.0671866 0.265643682 no value
0.254301 2388 PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FER (EC 2.7.1.112) (P94-FER) (C-FER). [SWISSPROT;Acc:P16591] 0.0558685 0.219694378 FER
0.254478 1940 "ISOLEUCYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.5) (ISOLEUCINE--TRNA LIGASE) (ILERS) (IRS). [SWISSPROT;Acc:P41252]" 0.0589414 0.231616878 no value
1941 IARS2
0.25461 1587 0.0612982 0.240753309 CHAC1
0.25466 2069 0.0584321 0.229451425 ZCCHC4
0.254881 2979 HOMEOBOX PROTEIN HOX-B5 (HOX-2A) (HHO.C10) (HU-1). [SWISSPROT;Acc:P09067] 0.035571 0.139559245 HOXB5
0.254965 461 TRANSCRIPTIONAL CO-ACTIVATOR WITH PDZ-BINDING MOTIF (TAZ). [RefSeq;Acc:NM_015472] 0.0702636 0.275581354 WWTR1

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/