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 1902 to 1951 of 3206 in total
Rank
description
measured
expected
final
Hugo
1902 0.549308 2.36366 0.232397214 no value
1903 "SERINE HYDROXYMETHYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.2.1) (SERINE METHYLASE) (GLYCINE HYDROXYMETHYLTRANSFERASE) (SHMT). [SWISSPROT;Acc:P34897]" 0.413255 1.77935 0.232250541 SHMT2
1904 DNA-DIRECTED RNA POLYMERASE II 23 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB25) (XAP4) (RPB5) (RPABC1). [SWISSPROT;Acc:P19388] 0.465033 2.00245 0.232232016 POLR2E
1905 "UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.10.2.2) (RIESKE IRON-SULFUR PROTEIN) (RISP). [SWISSPROT;Acc:P47985]" 0.102272 0.440396 0.232227359 UQCRFSL1
1906 SUPPRESSOR OF TY 5 HOMOLOG; SUPPRESSOR OF TY (S.CEREVISIAE) 5 HOMOLOG. [RefSeq;Acc:NM_003169] 1.04135 4.48455 0.23220836 no value
1907 0.0196837 0.0847765 0.232183447 LTV1
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

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/