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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measured Gene Rank Hugo description expected final
Results: HTML CSV LaTeX Showing element 2058 to 2107 of 3206 in total
measured
Rank
Hugo
description
expected
final
0.18122 1811 ACY1 AMINOACYLASE-1 (EC 3.5.1.14) (N-ACYL-L-AMINO-ACID AMIDOHYDROLASE) (ACY-1). [SWISSPROT;Acc:Q03154] 0.773023 0.234430282
0.181398 202 KIN HSKIN17 PROTEIN. [RefSeq;Acc:NM_012311] 0.563416 0.321961038
0.181797 573 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]" 0.671805 0.270609775
0.182131 801 RFXANK DNA-BINDING PROTEIN RFXANK (REGULATORY FACTOR X SUBUNIT B) (RFX-B) (ANKYRIN REPEAT FAMILY A PROTEIN 1). [SWISSPROT;Acc:O14593] 0.695125 0.262011868
0.182207 1839 RPS24 40S RIBOSOMAL PROTEIN S24 (S19). [SWISSPROT;Acc:P16632] 0.780167 0.233548715
0.18221 2379 HLCS BIOTIN--PROTEIN LIGASE (EC 6.3.4.-) (BIOTIN APO-PROTEIN LIGASE) [INCLUDES: BIOTIN--[METHYLMALONYL-COA-CARBOXYLTRANSFERASE] LIGASE (EC 6.3.4.9); BIOTIN--[PROPIONYL-COA-CARBOXYLASE [ATP-HYDROLYZING]] LIGASE (EC 6.3.4.10) (HOLOCARBOXYLASE SYNTHETASE) (HCS); 0.828912 0.219818268
0.18235 2318 PMM2 PHOSPHOMANNOMUTASE 2 (EC 5.4.2.8) (PMM 2). [SWISSPROT;Acc:O15305] 0.82204 0.221826189
0.18248 1711 PNPLA7 0.768033 0.237593958
0.182551 440 GSTT2B GLUTATHIONE S-TRANSFERASE THETA 2 (EC 2.5.1.18) (GST CLASS-THETA). [SWISSPROT;Acc:P30712] 0.659693 0.276721142
0.182783 113 ARID1A "SWI/SNF-RELATED, MATRIX-ASSOCIATED, ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY F MEMBER 1 (SWI-SNF COMPLEX PROTEIN P270) (B120). [SWISSPROT;Acc:O14497]" 0.506093 0.361164845
114 PDCD6 PROGRAMMED CELL DEATH PROTEIN 6 (PROBABLE CALCIUM-BINDING PROTEIN ALG- 2). [SWISSPROT;Acc:O75340]
0.183128 296 MAGI1 BAI1-ASSOCIATED PROTEIN 1; WW DOMAIN-CONTAINING PROTEIN 3; ATROPHIN-1 INTERACTING PROTEIN 3. [RefSeq;Acc:NM_004742] 0.60884 0.300781815
0.183159 505 IMPDH1 INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 1 (EC 1.1.1.205) (IMP DEHYDROGENASE 1) (IMPDH-I) (IMPD 1). [SWISSPROT;Acc:P20839] 0.66836 0.274042432
0.183185 2274 MTRF1L MITOCHONDRIAL TRANSLATIONAL RELEASE FACTOR 1-LIKE. [RefSeq;Acc:NM_019041] 0.822563 0.222700267
0.183187 1460 ADD1 ALPHA ADDUCIN (ERYTHROCYTE ADDUCIN ALPHA SUBUNIT). [SWISSPROT;Acc:P35611] 0.753661 0.243062862
0.183433 1816 UNC119 UNC-119 PROTEIN HOMOLOG (RETINAL PROTEIN 4) (HRG4). [SWISSPROT;Acc:Q13432] 0.783008 0.234267083
0.18361 1377 HHEX HOMEOBOX PROTEIN PRH (HEMATOPOIETICALLY EXPRESSED HOMEOBOX) (HOMEOBOX PROTEIN HEX). [SWISSPROT;Acc:Q03014] 0.750509 0.244647299
0.183757 1456 ADD3 GAMMA ADDUCIN (ADDUCIN-LIKE PROTEIN 70). [SWISSPROT;Acc:Q9UEY8] 0.755771 0.243138464
0.183942 2312 AP3M2 ADAPTER-RELATED PROTEIN COMPLEX 3 MU 2 SUBUNIT (CLATHRIN COAT ASSEMBLY PROTEIN AP47 HOMOLOG 2) (CLATHRIN COAT ASSOCIATED PROTEIN AP47 HOMOLOG 2) (GOLGI ADAPTOR AP-1 47 KDA PROTEIN HOMOLOG 2) (HA1 47 KDA SUBUNIT HOMOLOG 2) (CLATHRIN ASSEMBLY PROTEIN ASSEMB 0.828397 0.22204571
0.183967 198 PXN PAXILLIN. [SWISSPROT;Acc:P49023] 0.570423 0.322509787
0.184055 1888 PRPF18 PRP18 PRE-MRNA PROCESSING FACTOR 18 HOMOLOG. [RefSeq;Acc:NM_003675] 0.790803 0.232744438
0.184777 2894 PKM2 "PYRUVATE KINASE, M1 ISOZYME (EC 2.7.1.40) (PYRUVATE KINASE MUSCLE ISOZYME) (CYTOSOLIC THYROID HORMONE-BINDING PROTEIN) (CTHBP) (THBP1). [SWISSPROT;Acc:P14618]" 1.05445 0.175235431
0.184799 1033 CTSL1 CATHEPSIN L PRECURSOR (EC 3.4.22.15) (MAJOR EXCRETED PROTEIN) (MEP). [SWISSPROT;Acc:P07711] 0.729445 0.253341924
0.184877 2408 APIP 0.845209 0.218735248
0.184977 1556 no value 0.766628 0.241286517
0.185143 186 KCTD9 0.561582 0.329681151
0.18522 1786 ARG2 "ARGINASE II, MITOCHONDRIAL PRECURSOR (EC 3.5.3.1) (NON-HEPATIC ARGINASE) (KIDNEY-TYPE ARGINASE). [SWISSPROT;Acc:P78540]" 0.787708 0.235137894
0.185296 2085 RUVBL1 RUVB-LIKE 1 (EC 3.6.1.-) (49-KDA TATA BOX-BINDING PROTEIN-INTERACTING PROTEIN) (49 KDA TBP-INTERACTING PROTEIN) (TIP49A) (PONTIN 52) (NUCLEAR MATRIX PROTEIN 238) (NMP 238) (54 KDA ERYTHROCYTE CYTOSOLIC PROTEIN) (ECP-54) (TIP60-ASSOCIATED PROTEIN 54-ALPHA) 0.809316 0.228953833
0.185352 1023 TRPC4 SHORT TRANSIENT RECEPTOR POTENTIAL CHANNEL 4 (TRPC4) (TRP-RELATED PROTEIN 4) (HTRP-4) (HTRP4). [SWISSPROT;Acc:Q9UBN4] 0.731277 0.253463462
0.185372 2939 CBX1 CHROMOBOX PROTEIN HOMOLOG 1 (HETEROCHROMATIN PROTEIN 1 HOMOLOG BETA) (HP1 BETA) (MODIFIER 1 PROTEIN) (M31) (HETEROCHROMATIN PROTEIN P25). [SWISSPROT;Acc:P23197] 1.18579 0.156327849
0.185899 96 KCNA1 POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 1 (POTASSIUM CHANNEL KV1.1) (HUKI) (HBK1). [SWISSPROT;Acc:Q09470] 0.494524 0.375915021
0.186417 1188 TGFBR1 TGF-BETA RECEPTOR TYPE I PRECURSOR (EC 2.7.1.37) (TGFR-1) (TGF-BETA TYPE I RECEPTOR) (SERINE/THREONINE-PROTEIN KINASE RECEPTOR R4) (SKR4) (ACTIVIN RECEPTOR-LIKE KINASE 5) (ALK-5). [SWISSPROT;Acc:P36897] 0.74967 0.248665413
0.187173 41 CUTL1 CCAAT DISPLACEMENT PROTEIN (CDP) (CUT-LIKE 1). [SWISSPROT;Acc:P39880] 0.444789 0.420813015
0.187278 2323 RPS21 40S RIBOSOMAL PROTEIN S21. [SWISSPROT;Acc:P35265] 0.844371 0.221795869
0.18745 3063 GNB4 GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT 4 (TRANSDUCIN BETA CHAIN 4). [SWISSPROT;Acc:Q9HAV0] 1.78008 0.105304256
0.187564 1841 no value 60S RIBOSOMAL PROTEIN L39. [SWISSPROT;Acc:P02404] 0.803133 0.233540397
1842 RPL31 60S RIBOSOMAL PROTEIN L31. [SWISSPROT;Acc:P12947]
1843 RPS19 40S RIBOSOMAL PROTEIN S19. [SWISSPROT;Acc:P39019]
0.187708 151 KHDRBS2 "KH DOMAIN-CONTAINING, RNA-BINDING, SIGNAL TRANSDUCTION-ASSOCIATED PROTEIN 2; SAM68-LIKE MAMMALIAN PROTEIN 1. [RefSeq;Acc:NM_152688]" 0.534375 0.351266433
0.188344 2283 GDPD1 0.846836 0.222409061
0.188365 770 CDC37 HSP90 CO-CHAPERONE CDC37 (HSP90 CHAPERONE PROTEIN KINASE-TARGETING SUBUNIT) (P50CDC37). [SWISSPROT;Acc:Q16543] 0.715239 0.26335952
0.188445 1353 RNF20 RING FINGER PROTEIN 20. [RefSeq;Acc:NM_019592] 0.768755 0.245130113
1354 RNF40 RING FINGER PROTEIN 40; 95 KDA RETINOBLASTOMA PROTEIN BINDING PROTEIN; LIKELY ORTHOLOG OF RAT STARING. [RefSeq;Acc:NM_014771]
0.188839 2844 CLEC3A C-TYPE LECTIN SUPERFAMILY MEMBER 1 PRECURSOR (CARTILAGE-DERIVED C-TYPE LECTIN). [SWISSPROT;Acc:O75596] 0.981321 0.192433465
0.189161 1102 PRKRAP1 "PROTEIN KINASE, INTERFERON-INDUCIBLE DOUBLE STRANDED RNA DEPENDENT ACTIVATOR; PROTEIN ACTIVATOR OF THE INTERFERON-INDUCED PROTEIN KINASE. [RefSeq;Acc:NM_003690]" 0.753541 0.251029473
0.189189 2804 HTATIP2 "HIV-1 TAT INTERACTIVE PROTEIN 2, 30KDA; TAT-INTERACTING PROTEIN (30KD); HIV-1 TAT INTERACTIVE PROTEIN 2, 30 KDA; HIV-1 TAT INTERACTIVE PROTEIN 2, 30 KD. [RefSeq;Acc:NM_006410]" 0.954128 0.198284717
0.189314 2813 OTUB1 UBIQUITIN-SPECIFIC PROTEASE OTUBAIN 1. [RefSeq;Acc:NM_017670] 0.96599 0.195979254
0.189368 1087 RPAP3 0.752124 0.251777632
0.189451 1183 UBC UBIQUITIN. [SWISSPROT;Acc:P02248] 0.761637 0.248741855
0.190544 1626 PRKACG "CAMP-DEPENDENT PROTEIN KINASE, GAMMA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-GAMMA). [SWISSPROT;Acc:P22612]" 0.796037 0.239365758

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/