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 1758 to 1807 of 3206 in total
Rank
description
measured
expected
final
Hugo
1758 "DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 39 ISOFORM 1; NUCLEAR RNA HELICASE, DECD VARIANT OF DEAD BOX FAMILY. [RefSeq;Acc:NM_005804]" 0.0299559 0.126548 0.236715713 DDX39
1759 "VACUOLAR ATP SYNTHASE SUBUNIT B, KIDNEY ISOFORM (EC 3.6.3.14) (V- ATPASE B1 SUBUNIT) (VACUOLAR PROTON PUMP B ISOFORM 1) (ENDOMEMBRANE PROTON PUMP 58 KDA SUBUNIT). [SWISSPROT;Acc:P15313]" 0.299765 1.26636 0.236713889 ATP6V1B1
1760 VACUOLAR ATP SYNTHASE SUBUNIT F (EC 3.6.3.14) (V-ATPASE F SUBUNIT) (VACUOLAR PROTON PUMP F SUBUNIT) (V-ATPASE 14 KDA SUBUNIT). [SWISSPROT;Acc:Q16864] 0.424679 1.79432 0.236679634 ATP6V1F
1761 O-SIALOGLYCOPROTEIN ENDOPEPTIDASE. [RefSeq;Acc:NM_017807] 0.346601 1.46589 0.236444072 OSGEP
1762 RUVB-LIKE 2 (EC 3.6.1.-) (48-KDA TATA BOX-BINDING PROTEIN-INTERACTING PROTEIN) (48-KDA TBP-INTERACTING PROTEIN) (TIP49B) (REPRESSING PONTIN 52) (REPTIN 52) (51 KDA ERYTHROCYTE CYTOSOLIC PROTEIN) (ECP-51) (TIP60-ASSOCIATED PROTEIN 54-BETA) (TAP54-BETA) (CG 0.245894 1.04017 0.236397896 RUVBL2
1763 "ATPASE, H+ TRANSPORTING, LYSOSOMAL 38KDA, V0 SUBUNIT D ISOFORM 2. [RefSeq;Acc:NM_152565]" 0.33278 1.40872 0.236228633 ATP6V0D2
1764 0.0607427 0.257167 0.236199435 no value
1765 GLUTATHIONE S-TRANSFERASE P (EC 2.5.1.18) (GST CLASS-PI) (GSTP1-1). [SWISSPROT;Acc:P09211] 0.208499 0.882968 0.236134265 GSTP1
1766 "DJ850E9.1 (NOVEL C2H2 TYPE ZINC FINGER PROTEIN SIMILAR TO DROSOPHILA SCRATCH (SCRT), SLUG AND XENOPUS SNAIL) (FRAGMENT). [SPTREMBL;Acc:Q9NQ03]" 0.281698 1.1936 0.236007038 no value
1767 THYROID RECEPTOR INTERACTING PROTEIN 12 (TRIP12). [SWISSPROT;Acc:Q14669] 0.0325717 0.138013 0.236004579 TRIP12
1768 "DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX, MITOCHONDRIAL PRECURSOR (EC 2.3.1.61) (E2) (E2K). [SWISSPROT;Acc:P36957]" 0.660595 2.79908 0.23600433 DLSTP
1769 PEROXISOMAL MEMBRANE PROTEIN 2 (22 KDA PEROXISOMAL MEMBRANE PROTEIN). [SWISSPROT;Acc:Q9NR77] 0.0420153 0.178036 0.235993282 PXMP2
1770 HEAT SHOCK-RELATED 70 KDA PROTEIN 2 (HEAT SHOCK 70 KDA PROTEIN 2). [SWISSPROT;Acc:P54652] 0.0660691 0.279962 0.235993099 HSPA2
1771 HEAT SHOCK COGNATE 71 KDA PROTEIN. [SWISSPROT;Acc:P11142] 0.126046 0.534109 0.235993028 HSPA8
1772 HEAT SHOCK 70 KDA PROTEIN 1 (HSP70.1) (HSP70-1/HSP70-2). [SWISSPROT;Acc:P08107] 0.0654179 0.277203 0.235992756 no value
1773 "RIBOSOMAL PROTEIN P0-LIKE PROTEIN; 60S ACIDIC RIBOSOMAL PROTEIN PO; RIBOSOMAL PROTEIN, LARGE, P0-LIKE. [RefSeq;Acc:NM_016183]" 0.797221 3.37861 0.235961238 MRTO4
1774 "DIHYDROLIPOAMIDE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.8.1.4) (GLYCINE CLEAVAGE SYSTEM L PROTEIN). [SWISSPROT;Acc:P09622]" 0.596138 2.52689 0.23591767 DLD
1775 SCRATCH; SCRATCH 1. [RefSeq;Acc:NM_031309] 0.322861 1.36866 0.235895694 no value
1776 0.103336 0.438523 0.235645565 WDR70
1777 CDA11 PROTEIN. [RefSeq;Acc:NM_032026] 0.378654 1.60733 0.235579501 TATDN1
1778 ARGININOSUCCINATE SYNTHASE (EC 6.3.4.5) (CITRULLINE--ASPARTATE LIGASE). [SWISSPROT;Acc:P00966] 0.161564 0.685844 0.235569605 ASS1
1779 RETINOL DEHYDROGENASE 8 (ALL-TRANS); PHOTORECEPTOR OUTER SEGMENT ALL-TRANS RETINOL DEHYDROGENASE. [RefSeq;Acc:NM_015725] 0.0319409 0.135713 0.23535623 RDH8
1780 ADENINE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.7) (APRT). [SWISSPROT;Acc:P07741] 0.273997 1.16418 0.235356216 no value
1781 ESTRADIOL 17 BETA-DEHYDROGENASE 1 (EC 1.1.1.62) (17-BETA-HSD 1) (PLACENTAL 17-BETA-HYDROXYSTEROID DEHYDROGENASE) (20 ALPHA- HYDROXYSTEROID DEHYDROGENASE) (20-ALPHA-HSD) (E2DH). [SWISSPROT;Acc:P14061] 0.0258082 0.109656 0.235356022 HSD17B1
1782 17 BETA-HYDROXYSTEROID DEHYDROGENASE. [SPTREMBL;Acc:Q13034] 0.024834 0.105517 0.23535544 no value
1783 PUTATIVE SIALOGLYCOPROTEASE TYPE 2. [RefSeq;Acc:NM_022353] 0.365106 1.55176 0.235285096 OSGEPL1
1784 "C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC (C1-THF SYNTHASE) [INCLUDES: METHYLENETETRAHYDROFOLATE DEHYDROGENASE (EC 1.5.1.5); METHENYLTETRAHYDROFOLATE CYCLOHYDROLASE (EC 3.5.4.9); FORMYLTETRAHYDROFOLATE SYNTHETASE (EC 6.3.4.3)]. [SWISSPROT;Acc:P115" 0.156153 0.663781 0.23524777 MTHFD1
1785 S-ADENOSYLMETHIONINE SYNTHETASE GAMMA FORM (EC 2.5.1.6) (METHIONINE ADENOSYLTRANSFERASE) (ADOMET SYNTHETASE) (MAT-II). [SWISSPROT;Acc:P31153] 0.51691 2.19829 0.23514186 MAT2A
1786 "ARGINASE II, MITOCHONDRIAL PRECURSOR (EC 3.5.3.1) (NON-HEPATIC ARGINASE) (KIDNEY-TYPE ARGINASE). [SWISSPROT;Acc:P78540]" 0.18522 0.787708 0.235137894 ARG2
1787 PREFOLDIN SUBUNIT 3 (VON HIPPEL-LINDAU BINDING PROTEIN 1) (VHL BINDING PROTEIN-1) (VBP-1) (HIBBJ46). [SWISSPROT;Acc:Q15765] 0.0305539 0.129981 0.235064356 VBP1
1788 UXT PROTEIN (UBIQUITOUSLY EXPRESSED TRANSCRIPT PROTEIN) (HSPC024). [SWISSPROT;Acc:Q9UBK9] UXT
1789 PREFOLDIN SUBUNIT 2 (HSPC231). [SWISSPROT;Acc:Q9UHV9] 0.15115 0.643016 0.235064135 PFDN2
1790 ARGINASE 1 (EC 3.5.3.1) (LIVER-TYPE ARGINASE). [SWISSPROT;Acc:P05089] 0.222245 0.945747 0.234994137 ARG1
1791 DNA-DIRECTED RNA POLYMERASES III 12.5 KDA POLYPEPTIDE (EC 2.7.7.6) (RNA POLYMERASE III C11 SUBUNIT) (HSC11P) (HRPC11) (MY010 PROTEIN). [SWISSPROT;Acc:Q9Y2Y1] 0.163024 0.693873 0.234947894 POLR3K
1792 DIMERIC DIHYDRODIOL DEHYDROGENASE; 3-DEOXYGLUCOSONE REDUCTASE. [RefSeq;Acc:NM_014475] 0.0986496 0.419992 0.234884474 DHDH
1793 "HEXAPRENYLDIHYDROXYBENZOATE METHYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.1.114) (DIHYDROXYHEXAPRENYLBENZOATE METHYLTRANSFERASE) (3,4- DIHYDROXY-5-HEXAPRENYLBENZOATE METHYLTRANSFERASE) (DHHB METHYLTRANSFERASE) (DHHB-MT) (DHHB-MTASE). [SWISSPRO" 0.0303966 0.129436 0.234838839 COQ3
1794 GUANINE DEAMINASE (EC 3.5.4.3) (GUANASE) (GUANINE AMINASE) (GUANINE AMINOHYDROLASE) (GAH) (P51-NEDASIN). [SWISSPROT;Acc:Q9Y2T3] 0.234676 0.999309 0.234838273 GDA
1795 "ATP SYNTHASE COUPLING FACTOR B, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:Q99766]" 0.0303657 0.129305 0.234837787 ATP5S
1796 PROGRAMMED CELL DEATH PROTEIN 5 (TFAR19 PROTEIN) (TF-1 CELL APOPTOSIS RELATED GENE-19 PROTEIN). [SWISSPROT;Acc:O14737] 0.218499 0.930463 0.234828252 PDCD5
1797 DNA TOPOISOMERASE III ALPHA (EC 5.99.1.2). [SWISSPROT;Acc:Q13472] 0.09162 0.390211 0.234796046 TOP3A
1798 "FOLYLPOLYGLUTAMATE SYNTHASE, MITOCHONDRIAL PRECURSOR (EC 6.3.2.17) (FOLYLPOLY-GAMMA-GLUTAMATE SYNTHETASE) (FPGS). [SWISSPROT;Acc:Q05932]" 0.107427 0.457652 0.234735126 FPGS
1799 0.0461397 0.196587 0.234703719 FAM57B
1800 0.0580492 0.247338 0.234695841 no value
1801 MEMBRANE PROTEIN EXPRESSED IN EPITHELIAL-LIKE LUNG ADENOCARCINOMA. [RefSeq;Acc:NM_024792] FAM57A
1802 RAN BINDING PROTEIN 11. [RefSeq;Acc:NM_016338] 0.0547985 0.233549 0.234633846 IPO11
1803 HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE; HUMAN GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE. [RefSeq;Acc:NM_004712] 0.24593 1.0482 0.234621255 HGS
1804 CONSERVED OLIGOMERIC GOLGI COMPLEX COMPONENT 7. [SWISSPROT;Acc:P83436] 0.0361228 0.153963 0.234620006 COG7
1805 GTP CYCLOHYDROLASE I (EC 3.5.4.16) (GTP-CH-I). [SWISSPROT;Acc:P30793] 0.250702 1.06873 0.234579361 GCH1
1806 P53-RELATED PROTEIN KINASE (EC 2.7.1.-) (NORI-2). [SWISSPROT;Acc:Q96S44] 0.131908 0.562339 0.23457025 TP53RK
1807 "EARLY ENDOSOME ANTIGEN 1, 162KD; EARLY ENDOSOME-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_003566]" 0.0387072 0.165025 0.234553552 EEA1

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/