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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final Gene expected Rank measured description Hugo
Results: HTML CSV LaTeX Showing element 1251 to 1300 of 3206 in total
final
expected
Rank
measured
description
Hugo
0.231256051 0.165264 1956 0.0382183 60S RIBOSOMAL PROTEIN L34. [SWISSPROT;Acc:P49207] RPL34
0.231256174 0.247999 1955 0.0573513 SERINE RACEMASE (EC 5.1.1.-). [SWISSPROT;Acc:Q9GZT4] SRR
0.231256346 5.73234 1954 1.32564 PROTEIN TRANSPORT PROTEIN SEC61 ALPHA SUBUNIT ISOFORM 1 (SEC61 ALPHA- 1). [SWISSPROT;Acc:P38378] SEC61A1
0.231256577 0.247068 1953 0.0571361 60S RIBOSOMAL PROTEIN L14 (CAG-ISL 7). [SWISSPROT;Acc:P50914] no value
0.231271592 0.554305 1952 0.128195 RIBOSE 5-PHOSPHATE ISOMERASE (EC 5.3.1.6) (PHOSPHORIBOISOMERASE). [SWISSPROT;Acc:P49247] RPIA
0.231287163 3.54858 1951 0.820741 DNA-DIRECTED RNA POLYMERASE I 135 KDA POLYPEPTIDE (EC 2.7.7.6) (RNA POLYMERASE I SUBUNIT 2) (RPA135). [SWISSPROT;Acc:Q9H9Y6] POLR1B
0.231320896 0.0821011 1950 0.0189917 ESF1
0.231321224 2.82208 1949 0.652807 40S RIBOSOMAL PROTEIN S11. [SWISSPROT;Acc:P04643] RPS11
0.231352492 1.93857 1948 0.448493 TRUB PSEUDOURIDINE (PSI) SYNTHASE HOMOLOG 1. [RefSeq;Acc:NM_139169] TRUB1
0.231413557 2.81057 1947 0.650404 MITOCHONDRIAL RIBOSOMAL PROTEIN L4 ISOFORM A. [RefSeq;Acc:NM_015956] MRPL4
0.231420118 0.920283 1946 0.212972 PRE-MRNA CLEAVAGE COMPLEX II PROTEIN CLP1. [SWISSPROT;Acc:Q92989] CLP1
0.231568504 5.71481 1945 1.32337 60S RIBOSOMAL PROTEIN L26. [SWISSPROT;Acc:Q02877] RPL26
0.231598285 5.7155 1944 1.3237 MITOCHONDRIAL RIBOSOMAL PROTEIN L2. [RefSeq;Acc:NM_015950] MRPL2
0.231599281 5.71513 1943 1.32362 40S RIBOSOMAL PROTEIN S15 (RIG PROTEIN). [SWISSPROT;Acc:P11174] no value
0.231604586 5.59596 1942 1.29605 60S RIBOSOMAL PROTEIN L35. [SWISSPROT;Acc:P42766] RPL35
0.231616878 0.254478 1940 0.0589414 "ISOLEUCYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.5) (ISOLEUCINE--TRNA LIGASE) (ILERS) (IRS). [SWISSPROT;Acc:P41252]" no value
1941 IARS2
0.231631889 2.5639 1939 0.593881 DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE (EC 2.7.7.6) (RNA POLYMERASE II SUBUNIT 2) (RPB2). [SWISSPROT;Acc:P30876] POLR2B
0.231678493 1.70248 1938 0.394428 GUF1
0.231690359 1.1607 1937 0.268923 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM7. [SWISSPROT;Acc:Q9UK45] no value
0.231690563 5.32089 1936 1.2328 EPITHELIAL-CADHERIN PRECURSOR (E-CADHERIN) (UVOMORULIN) (CADHERIN-1) (CAM 120/80). [SWISSPROT;Acc:P12830] CDH1
0.231690854 5.38515 1935 1.24769 C367G8.3 (NOVEL PROTEIN SIMILAR TO RPL23A (60S RIBOSOMAL PROTEIN L23A)) (60S RIBOSOMAL PROTEIN L23A LIKE). [SPTREMBL;Acc:Q9BR02] no value
0.231696263 6.05655 1934 1.40328 60S RIBOSOMAL PROTEIN L23A. [SWISSPROT;Acc:P29316]
0.23171353 0.120529 1933 0.0279282 FAM98A
0.231713775 0.361827 1932 0.0838403 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] PUF60
0.23171431 0.104981 1931 0.0243256 FAM98B
0.231714313 0.136317 1930 0.0315866 CWF19L2
0.231714934 0.529927 1929 0.122792 MULTISYNTHETASE COMPLEX AUXILIARY COMPONENT P38 (JTV-1 PROTEIN) (PRO0992). [SWISSPROT;Acc:Q13155] no value
0.231778704 3.04081 1928 0.704795
0.23178806 3.09201 1927 0.716691 60S RIBOSOMAL PROTEIN L32. [SWISSPROT;Acc:P02433] SNORA7A
0.231805771 2.13521 1926 0.494954 "SERINE HYDROXYMETHYLTRANSFERASE, CYTOSOLIC (EC 2.1.2.1) (SERINE METHYLASE) (GLYCINE HYDROXYMETHYLTRANSFERASE) (SHMT). [SWISSPROT;Acc:P34896]" SHMT1
0.231823225 0.565103 1925 0.131004 METAXIN 2. [SWISSPROT;Acc:O75431] MTX2
0.231957345 0.828592 1924 0.192198 POLYMERASE (RNA) III (DNA DIRECTED) (62KD). [RefSeq;Acc:NM_006468] POLR3C
0.231959026 0.419969 1923 0.0974156 "SOLUTE CARRIER FAMILY 35, MEMBER B1; UDP-GALACTOSE TRANSPORTER RELATED. [RefSeq;Acc:NM_005827]" SLC35B1
0.231969422 0.0707964 1922 0.0164226 CHOLINEPHOSPHATE CYTIDYLYLTRANSFERASE B (EC 2.7.7.15) (PHOSPHORYLCHOLINE TRANSFERASE B) (CTP:PHOSPHOCHOLINE CYTIDYLYLTRANSFERASE B) (CT B) (CCT B) (CCT-BETA). [SWISSPROT;Acc:Q9Y5K3] PCYT1B
0.231969642 0.317545 1921 0.0736608 FAD SYNTHETASE. [RefSeq;Acc:NM_025207] FLAD1
0.231969671 2.13396 1920 0.495014 LIGATIN (HEPATOCELLULAR CARCINOMA-ASSOCIATED ANTIGEN 56). [SWISSPROT;Acc:P41214] LGTN
0.231970222 0.0807026 1917 0.0187206 NADPH-CYTOCHROME P450 REDUCTASE (EC 1.6.2.4) (CPR) (P450R). [SWISSPROT;Acc:P16435] 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
0.231970338 0.0754368 1916 0.0174991 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 no value
0.232026712 0.208298 1915 0.0483307 TYROSYL-TRNA SYNTHETASE (EC 6.1.1.1) (TYROSYL--TRNA LIGASE) (TYRRS). [SWISSPROT;Acc:P54577] YARS
0.232031559 0.737404 1914 0.171101 DNA-DIRECTED RNA POLYMERASES III 39 KDA POLYPEPTIDE (EC 2.7.7.6) (RNA POLYMERASE III C39 SUBUNIT). [SWISSPROT;Acc:Q9H1D9] POLR3F
0.232079471 0.35711 1913 0.0828779 HISTONE H4. [SWISSPROT;Acc:P02304] no value
0.232097856 1.87377 1912 0.434898 "ADENYLATE KINASE ISOENZYME 2, MITOCHONDRIAL (EC 2.7.4.3) (ATP-AMP TRANSPHOSPHORYLASE). [SWISSPROT;Acc:P54819]" AK2
0.232103402 0.730041 1911 0.169445 MITOCHONDRIAL 60S RIBOSOMAL PROTEIN L27 (L27MT) (HSPC250). [SWISSPROT;Acc:Q9P0M9] MRPL27
0.232133423 0.274826 1910 0.0637963 "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" PRDX5
0.232177358 5.86431 1909 1.36156 MITOCHONDRIAL 60S RIBOSOMAL PROTEIN L3 (L3MT). [SWISSPROT;Acc:P09001] MRPL3
0.232182447 6.5312 1908 1.51643 40S RIBOSOMAL PROTEIN S3. [SWISSPROT;Acc:P23396] RPS3
0.232183447 0.0847765 1907 0.0196837 LTV1

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/