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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Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 1908 to 1957 of 3206 in total
Rank
description
measured
expected
final
Hugo
1908 40S RIBOSOMAL PROTEIN S3. [SWISSPROT;Acc:P23396] 1.51643 6.5312 0.232182447 RPS3
1909 MITOCHONDRIAL 60S RIBOSOMAL PROTEIN L3 (L3MT). [SWISSPROT;Acc:P09001] 1.36156 5.86431 0.232177358 MRPL3
1910 "PEROXIREDOXIN 5, MITOCHONDRIAL PRECURSOR (PRX-V) (PEROXISOMAL ANTIOXIDANT ENZYME) (PLP) (THIOREDOXIN PEROXIDASE PMP20) (ANTIOXIDANT ENZYME B166) (AOEB166) (TPX TYPE VI) (LIVER TISSUE 2D-PAGE SPOT 71B) (ALU CO-REPRESSOR 1) (SBBI10). [SWISSPROT;Acc:P" 0.0637963 0.274826 0.232133423 PRDX5
1911 MITOCHONDRIAL 60S RIBOSOMAL PROTEIN L27 (L27MT) (HSPC250). [SWISSPROT;Acc:Q9P0M9] 0.169445 0.730041 0.232103402 MRPL27
1912 "ADENYLATE KINASE ISOENZYME 2, MITOCHONDRIAL (EC 2.7.4.3) (ATP-AMP TRANSPHOSPHORYLASE). [SWISSPROT;Acc:P54819]" 0.434898 1.87377 0.232097856 AK2
1913 HISTONE H4. [SWISSPROT;Acc:P02304] 0.0828779 0.35711 0.232079471 no value
1914 DNA-DIRECTED RNA POLYMERASES III 39 KDA POLYPEPTIDE (EC 2.7.7.6) (RNA POLYMERASE III C39 SUBUNIT). [SWISSPROT;Acc:Q9H1D9] 0.171101 0.737404 0.232031559 POLR3F
1915 TYROSYL-TRNA SYNTHETASE (EC 6.1.1.1) (TYROSYL--TRNA LIGASE) (TYRRS). [SWISSPROT;Acc:P54577] 0.0483307 0.208298 0.232026712 YARS
1916 BIFUNCTIONAL 3'-PHOSPHOADENOSINE 5'-PHOSPHOSULFATE SYNTHETHASE 2 (PAPS SYNTHETHASE 2) (PAPSS 2) (SULFURYLASE KINASE 2) (SK2) (SK 2) [INCLUDES: SULFATE ADENYLYLTRANSFERASE (EC 2.7.7.4) (SULFATE ADENYLATE TRANSFERASE) (SAT) (ATP-SULFURYLASE); ADENYLYLSULFAT 0.0174991 0.0754368 0.231970338 no value
1917 NADPH-CYTOCHROME P450 REDUCTASE (EC 1.6.2.4) (CPR) (P450R). [SWISSPROT;Acc:P16435] 0.0187206 0.0807026 0.231970222 POR
1918 BIFUNCTIONAL 3'-PHOSPHOADENOSINE 5'-PHOSPHOSULFATE SYNTHETHASE 1 (PAPS SYNTHETHASE 1) (PAPSS 1) (SULFURYLASE KINASE 1) (SK1) (SK 1) [INCLUDES: SULFATE ADENYLYLTRANSFERASE (EC 2.7.7.4) (SULFATE ADENYLATE TRANSFERASE) (SAT) (ATP-SULFURYLASE); ADENYLYLSULFAT PAPSS1
1919 CHOLINEPHOSPHATE CYTIDYLYLTRANSFERASE A (EC 2.7.7.15) (PHOSPHORYLCHOLINE TRANSFERASE A) (CTP:PHOSPHOCHOLINE CYTIDYLYLTRANSFERASE A) (CT A) (CCT A) (CCT-ALPHA). [SWISSPROT;Acc:P49585] PCYT1A
1920 LIGATIN (HEPATOCELLULAR CARCINOMA-ASSOCIATED ANTIGEN 56). [SWISSPROT;Acc:P41214] 0.495014 2.13396 0.231969671 LGTN
1921 FAD SYNTHETASE. [RefSeq;Acc:NM_025207] 0.0736608 0.317545 0.231969642 FLAD1
1922 CHOLINEPHOSPHATE CYTIDYLYLTRANSFERASE B (EC 2.7.7.15) (PHOSPHORYLCHOLINE TRANSFERASE B) (CTP:PHOSPHOCHOLINE CYTIDYLYLTRANSFERASE B) (CT B) (CCT B) (CCT-BETA). [SWISSPROT;Acc:Q9Y5K3] 0.0164226 0.0707964 0.231969422 PCYT1B
1923 "SOLUTE CARRIER FAMILY 35, MEMBER B1; UDP-GALACTOSE TRANSPORTER RELATED. [RefSeq;Acc:NM_005827]" 0.0974156 0.419969 0.231959026 SLC35B1
1924 POLYMERASE (RNA) III (DNA DIRECTED) (62KD). [RefSeq;Acc:NM_006468] 0.192198 0.828592 0.231957345 POLR3C
1925 METAXIN 2. [SWISSPROT;Acc:O75431] 0.131004 0.565103 0.231823225 MTX2
1926 "SERINE HYDROXYMETHYLTRANSFERASE, CYTOSOLIC (EC 2.1.2.1) (SERINE METHYLASE) (GLYCINE HYDROXYMETHYLTRANSFERASE) (SHMT). [SWISSPROT;Acc:P34896]" 0.494954 2.13521 0.231805771 SHMT1
1927 60S RIBOSOMAL PROTEIN L32. [SWISSPROT;Acc:P02433] 0.716691 3.09201 0.23178806 SNORA7A
1928 0.704795 3.04081 0.231778704 no value
1929 MULTISYNTHETASE COMPLEX AUXILIARY COMPONENT P38 (JTV-1 PROTEIN) (PRO0992). [SWISSPROT;Acc:Q13155] 0.122792 0.529927 0.231714934
1930 0.0315866 0.136317 0.231714313 CWF19L2
1931 0.0243256 0.104981 0.23171431 FAM98B
1932 FUSE-BINDING PROTEIN-INTERACTING REPRESSOR ISOFORM B; SIAH BINDING PROTEIN 1; PYRIMIDINE TRACT BINDING SPLICING FACTOR; RO RIBONUCLEOPROTEIN-BINDING PROTEIN 1; POLY-U BINDING SPLICING FACTOR PUF60. [RefSeq;Acc:NM_014281] 0.0838403 0.361827 0.231713775 PUF60
1933 0.0279282 0.120529 0.23171353 FAM98A
1934 60S RIBOSOMAL PROTEIN L23A. [SWISSPROT;Acc:P29316] 1.40328 6.05655 0.231696263 no value
1935 C367G8.3 (NOVEL PROTEIN SIMILAR TO RPL23A (60S RIBOSOMAL PROTEIN L23A)) (60S RIBOSOMAL PROTEIN L23A LIKE). [SPTREMBL;Acc:Q9BR02] 1.24769 5.38515 0.231690854
1936 EPITHELIAL-CADHERIN PRECURSOR (E-CADHERIN) (UVOMORULIN) (CADHERIN-1) (CAM 120/80). [SWISSPROT;Acc:P12830] 1.2328 5.32089 0.231690563 CDH1
1937 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM7. [SWISSPROT;Acc:Q9UK45] 0.268923 1.1607 0.231690359 no value
1938 0.394428 1.70248 0.231678493 GUF1
1939 DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE (EC 2.7.7.6) (RNA POLYMERASE II SUBUNIT 2) (RPB2). [SWISSPROT;Acc:P30876] 0.593881 2.5639 0.231631889 POLR2B
1940 "ISOLEUCYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.5) (ISOLEUCINE--TRNA LIGASE) (ILERS) (IRS). [SWISSPROT;Acc:P41252]" 0.0589414 0.254478 0.231616878 no value
1941 IARS2
1942 60S RIBOSOMAL PROTEIN L35. [SWISSPROT;Acc:P42766] 1.29605 5.59596 0.231604586 RPL35
1943 40S RIBOSOMAL PROTEIN S15 (RIG PROTEIN). [SWISSPROT;Acc:P11174] 1.32362 5.71513 0.231599281 no value
1944 MITOCHONDRIAL RIBOSOMAL PROTEIN L2. [RefSeq;Acc:NM_015950] 1.3237 5.7155 0.231598285 MRPL2
1945 60S RIBOSOMAL PROTEIN L26. [SWISSPROT;Acc:Q02877] 1.32337 5.71481 0.231568504 RPL26
1946 PRE-MRNA CLEAVAGE COMPLEX II PROTEIN CLP1. [SWISSPROT;Acc:Q92989] 0.212972 0.920283 0.231420118 CLP1
1947 MITOCHONDRIAL RIBOSOMAL PROTEIN L4 ISOFORM A. [RefSeq;Acc:NM_015956] 0.650404 2.81057 0.231413557 MRPL4
1948 TRUB PSEUDOURIDINE (PSI) SYNTHASE HOMOLOG 1. [RefSeq;Acc:NM_139169] 0.448493 1.93857 0.231352492 TRUB1
1949 40S RIBOSOMAL PROTEIN S11. [SWISSPROT;Acc:P04643] 0.652807 2.82208 0.231321224 RPS11
1950 0.0189917 0.0821011 0.231320896 ESF1
1951 DNA-DIRECTED RNA POLYMERASE I 135 KDA POLYPEPTIDE (EC 2.7.7.6) (RNA POLYMERASE I SUBUNIT 2) (RPA135). [SWISSPROT;Acc:Q9H9Y6] 0.820741 3.54858 0.231287163 POLR1B
1952 RIBOSE 5-PHOSPHATE ISOMERASE (EC 5.3.1.6) (PHOSPHORIBOISOMERASE). [SWISSPROT;Acc:P49247] 0.128195 0.554305 0.231271592 RPIA
1953 60S RIBOSOMAL PROTEIN L14 (CAG-ISL 7). [SWISSPROT;Acc:P50914] 0.0571361 0.247068 0.231256577 no value
1954 PROTEIN TRANSPORT PROTEIN SEC61 ALPHA SUBUNIT ISOFORM 1 (SEC61 ALPHA- 1). [SWISSPROT;Acc:P38378] 1.32564 5.73234 0.231256346 SEC61A1
1955 SERINE RACEMASE (EC 5.1.1.-). [SWISSPROT;Acc:Q9GZT4] 0.0573513 0.247999 0.231256174 SRR
1956 60S RIBOSOMAL PROTEIN L34. [SWISSPROT;Acc:P49207] 0.0382183 0.165264 0.231256051 RPL34
1957 PROTEIN TRANSPORT PROTEIN SEC61 ALPHA SUBUNIT ISOFORM 2 (SEC61 ALPHA- 2). [SWISSPROT;Acc:Q9Y2R3] 1.30722 5.6527 0.23125586 SEC61A2

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/