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 measured Gene Rank description expected final
Results: HTML CSV LaTeX Showing element 208 to 257 of 3206 in total
Hugo  : no value
measured
Rank
description
expected
final
0.147283 1196 DIHYDROPYRIMIDINE DEHYDROGENASE [NADP+] PRECURSOR (EC 1.3.1.2) (DPD) (DHPDHASE) (DIHYDROURACIL DEHYDROGENASE) (DIHYDROTHYMINE DEHYDROGENASE). [SWISSPROT;Acc:Q12882] 0.5927 0.248495023
0.151451 2892 UBIQUITIN ACTIVATING ENZYME E1-LIKE PROTEIN. [RefSeq;Acc:NM_006395] 0.850269 0.178121277
0.151787 2698 ESTROGEN-RELATED RECEPTOR GAMMA (ESTROGEN RECEPTOR RELATED PROTEIN 3) (ERR GAMMA-2). [SWISSPROT;Acc:O75454] 0.730409 0.207810966
0.152054 267 0.494121 0.307726245
0.152328 542 PROTEIN REGULATOR OF CYTOKINESIS 1; PROTEIN REGULATING CYTOKINESIS 1. [RefSeq;Acc:NM_003981] 0.561935 0.271077616
0.152828 89 0.396725 0.385224022
0.155654 213 RD PROTEIN. [SWISSPROT;Acc:P18615] 0.485577 0.320554721
0.156444 2208 40S RIBOSOMAL PROTEIN S3A. [SWISSPROT;Acc:P49241] 0.694888 0.225135561
0.157068 1368 HISTONE H3.1 (H3/A) (H3/C) (H3/D) (H3/F) (H3/H) (H3/I) (H3/J) (H3/K) (H3/L). [SWISSPROT;Acc:P16106] 0.641454 0.244862453
0.157677 2435 MICROSOMAL SIGNAL PEPTIDASE 18 KDA SUBUNIT (EC 3.4.-.-) (SPASE 18 KDA SUBUNIT) (SPC18) (ENDOPEPTIDASE SP18). [SWISSPROT;Acc:P21378] 0.725721 0.217269447
0.159907 909 NEUROTRIMIN PRECURSOR (HNT). [SWISSPROT;Acc:Q9P121] 0.619267 0.258219799
0.160247 1683 NUCLEOLAR PROTEIN NOP5 (NUCLEOLAR PROTEIN 5) (NOP58) (HSPC120). [SWISSPROT;Acc:Q9Y2X3] 0.672842 0.238164383
0.161283 2827 ZINC FINGER IMPRINTED 2. [SWISSPROT;Acc:Q9NZV7] 0.833576 0.193483258
0.163856 3131 "MYOSIN VA (MYOSIN 5A) (DILUTE MYOSIN HEAVY CHAIN, NON-MUSCLE) (MYOSIN HEAVY CHAIN 12) (MYOXIN). [SWISSPROT;Acc:Q9Y4I1]" 2.39209 0.068499095
0.166892 1328 NIF3-LIKE PROTEIN 1 (AMYOTROPHIC LATERAL SCLEROSIS 2 CHROMOSOMAL REGION CANDIDATE GENE PROTEIN 1) (MY018 PROTEIN) (MDS015). [SWISSPROT;Acc:Q9GZT8] 0.679841 0.245486812
0.166963 680 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 5 (EC 2.7.1.-) (MAPK/ERK KINASE KINASE 5) (MEK KINASE 5) (MEKK 5) (APOPTOSIS SIGNAL- REGULATING KINASE 1) (ASK-1). [SWISSPROT;Acc:Q99683] 0.628521 0.265644266
0.16968 2115 "4-AMINOBUTYRATE AMINOTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.6.1.19) (GAMMA-AMINO-N-BUTYRATE TRANSAMINASE) (GABA TRANSAMINASE) (GABA AMINOTRANSFERASE) (GABA-AT) (GABA-T). [SWISSPROT;Acc:P80404]" 0.743642 0.22817431
0.173712 2903 60S RIBOSOMAL PROTEIN L22 (EPSTEIN-BARR VIRUS SMALL RNA ASSOCIATED PROTEIN) (EBER ASSOCIATED PROTEIN) (EAP) (HEPARIN BINDING PROTEIN HBP15). [SWISSPROT;Acc:P35268] 0.997527 0.174142655
0.174557 2902 TYROSINE AMINOTRANSFERASE (EC 2.6.1.5) (L-TYROSINE:2-OXOGLUTARATE AMINOTRANSFERASE) (TAT). [SWISSPROT;Acc:P17735] 0.999179 0.174700429
0.180388 2097 URIDINE KINASE-LIKE 1. [SWISSPROT;Acc:Q9NWZ5] 0.789739 0.228414704
0.184977 1556 0.766628 0.241286517
0.187564 1841 60S RIBOSOMAL PROTEIN L39. [SWISSPROT;Acc:P02404] 0.803133 0.233540397
0.193648 230 JUN DIMERIZATION PROTEIN. [RefSeq;Acc:NM_130469] 0.614336 0.315215127
0.194172 2489 0.898593 0.216084479
0.199227 1136 PHOSPHOLIPID SCRAMBLASE 3 (PL SCRAMBLASE 3) (CA(2+)-DEPENDENT PHOSPHOLIPID SCRAMBLASE 3). [SWISSPROT;Acc:Q9NRY6] 0.79556 0.250423601
0.199469 1882 "CREATINE KINASE, UBIQUITOUS MITOCHONDRIAL PRECURSOR (EC 2.7.3.2) (U- MTCK) (MIA-CK) (ACIDIC-TYPE MITOCHONDRIAL CREATINE KINASE). [SWISSPROT;Acc:P12532]" 0.856983 0.232757243
0.20255 658 U2 SMALL NUCLEAR RIBONUCLEOPROTEIN AUXILIARY FACTOR 35 KDA SUBUNIT RELATED-PROTEIN 1. [SWISSPROT;Acc:Q15695] 0.757899 0.267251969
0.207889 2180 "GLYCINE CLEAVAGE SYSTEM H PROTEIN, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:P23434]" 0.916816 0.22675106
0.20849 303 HPAII TINY FRAGMENTS LOCUS 9C. [RefSeq;Acc:NM_022727] 0.697153 0.299059174
0.214359 1844 60S RIBOSOMAL PROTEIN L18A. [SWISSPROT;Acc:Q02543] 0.917867 0.233540371
0.215243 452 "PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1 (EC 3.1.3.48) (PROTEIN-TYROSINE PHOSPHATASE 1B) (PTP-1B). [SWISSPROT;Acc:P18031]" 0.779889 0.27599184
0.217355 2962 TRANSFORMING PROTEIN N-RAS. [SWISSPROT;Acc:P01111] 1.48707 0.146163261
0.217383 1472 TRANSCRIPTION FACTOR-LIKE PROTEIN MORF4 (MORTALITY FACTOR 4) (CELLULAR SENESCENCE-RELATED PROTEIN 1) (SEN1). [SWISSPROT;Acc:Q9Y690] 0.894645 0.242982412
0.218752 1600 TRANSLIN. [SWISSPROT;Acc:Q15631] 0.911432 0.240009128
0.21933 1539 HISTONE H3.3 (H3.A) (H3.B) (H3.3Q). [SWISSPROT;Acc:P06351] 0.906671 0.241906932
0.221267 2238 0.988036 0.223946293
0.221383 1995 INTEGRAL MEMBRANE PROTEIN CII-3B. [SPTREMBL;Acc:O75609] 0.959291 0.230777731
0.228054 2331 40S RIBOSOMAL PROTEIN S27 (METALLOPAN-STIMULIN 1) (MPS-1). [SWISSPROT;Acc:P42677] 1.0307 0.221261279
0.229236 1743 40S RIBOSOMAL PROTEIN S28. [SWISSPROT;Acc:P25112] 0.968071 0.236796681
0.231369 55 0.562729 0.411155281
0.231616 2302 DNA DIRECTED RNA POLYMERASE II POLYPEPTIDE J-RELATED GENE ISOFORM 3; RPB11B1ALPHA PROTEIN; RPB11B1BETA; DNA-DIRECTED RNA POLYMERASE II SUBUNIT 11. [RefSeq;Acc:NM_032959] 1.04193 0.222295164
0.232016 306 ALPHA-1-ACID GLYCOPROTEIN 2 PRECURSOR (AGP 2) (OROSOMUCOID 2) (OMD 2). [SWISSPROT;Acc:P19652] 0.784548 0.295732065
0.232938 2303 DNA DIRECTED RNA POLYMERASE II POLYPEPTIDE J-RELATED GENE ISOFORM 1; RPB11B1ALPHA PROTEIN; RPB11B1BETA; DNA-DIRECTED RNA POLYMERASE II SUBUNIT 11. [RefSeq;Acc:NM_145325] 1.0479 0.222290295
0.236585 498 0.862726 0.274229593
0.239571 2492 1.11109 0.215617997
0.241123 304 UBIQUITIN. [SWISSPROT;Acc:P02248] 0.807018 0.298782679
0.241532 1889 DIHYDROFOLATE REDUCTASE (EC 1.5.1.3). [SWISSPROT;Acc:P00374] 1.03785 0.232723419
0.246538 2859 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE ALPHA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 1) (1-AGPAT 1) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-ALPHA) (LPAAT-ALPHA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 1) (G15 PROTEIN). [SWISSPROT;Acc:Q9 1.30479 0.188948413
0.253043 829 PURINE NUCLEOSIDE PHOSPHORYLASE (EC 2.4.2.1) (INOSINE PHOSPHORYLASE) (PNP). [SWISSPROT;Acc:P00491] 0.969143 0.261099755
0.253802 2117 HYDROXYINDOLE O-METHYLTRANSFERASE (EC 2.1.1.4) (HIOMT) (ACETYLSEROTONIN O-METHYLTRANSFERASE) (ASMT). [SWISSPROT;Acc:P46597] 1.11232 0.228173547

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/