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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
expected Gene Rank description measured final Hugo
Results: HTML CSV LaTeX Showing element 2852 to 2901 of 3206 in total
expected
Rank
description
measured
final
Hugo
1.98642 2098 "GLUTATHIONE REDUCTASE, MITOCHONDRIAL PRECURSOR (EC 1.8.1.7) (GR) (GRASE). [SWISSPROT;Acc:P00390]" 0.453634 0.228367616 GSR
1.98825 712 HISTONE DEACETYLASE 2 (HD2). [SWISSPROT;Acc:Q92769] 0.52666 0.264886206 no value
1.99055 560 ELAV-LIKE PROTEIN 3 (HU-ANTIGEN C) (HUC) (PARANEOPLASTIC CEREBELLAR DEGENERATION-ASSOCIATED ANTIGEN) (PARANEOPLASTIC LIMBIC ENCEPHALITIS ANTIGEN 21). [SWISSPROT;Acc:Q14576] 0.539175 0.270867348
1.99671 594 PHOSPHOACETYLGLUCOSAMINE MUTASE (EC 5.4.2.3) (PAGM) (ACETYLGLUCOSAMINE PHOSPHOMUTASE) (N-ACETYLGLUCOSAMINE-PHOSPHATE MUTASE) (PHOSPHOGLUCOMUTASE 3). [SWISSPROT;Acc:O95394] 0.537765 0.269325541 PGM3
1.99819 723 ACTIN-LIKE PROTEIN 3 (ACTIN-RELATED PROTEIN 3) (ACTIN-2). [SWISSPROT;Acc:P32391] 0.528875 0.264677033 ACTR3
2.00168 1505 PBK1 PROTEIN. [SPTREMBL;Acc:O76021] 0.485772 0.242682147 RSL1D1
2.00171 1879 VACUOLAR ATP SYNTHASE 21 KDA PROTEOLIPID SUBUNIT (EC 3.6.3.14) (HATPL). [SWISSPROT;Acc:Q99437] 0.465943 0.23277248 ATP6V0B
2.00245 1904 DNA-DIRECTED RNA POLYMERASE II 23 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB25) (XAP4) (RPB5) (RPABC1). [SWISSPROT;Acc:P19388] 0.465033 0.232232016 POLR2E
2.00343 247 TRANSCRIPTION FACTOR BTF3 HOMOLOG 3. [SWISSPROT;Acc:Q13892] 0.625831 0.312379769 no value
2.00736 2717 "SOLUTE CARRIER FAMILY 27 (FATTY ACID TRANSPORTER), MEMBER 4; FATTY ACID TRANSPORT PROTEIN 4. [RefSeq;Acc:NM_005094]" 0.416194 0.207334011 SLC27A4
2.00865 1856 GTP-BINDING NUCLEAR PROTEIN RAN (TC4) (RAN GTPASE) (ANDROGEN RECEPTOR- ASSOCIATED PROTEIN 24). [SWISSPROT;Acc:P17080] 0.46892 0.233450327 RANP1
2.01624 2558 ELONGATION FACTOR 2 (EF-2). [SWISSPROT;Acc:P13639] 0.432107 0.214313276 EEF2
2.01815 244 "5'-AMP-ACTIVATED PROTEIN KINASE, CATALYTIC ALPHA-2 CHAIN (EC 2.7.1.-) (AMPK ALPHA-2 CHAIN). [SWISSPROT;Acc:P54646]" 0.630538 0.312433664 PRKAA2
2.02294 1679 0.48192 0.23822753 KCTD2
2.02325 3157 PYRROLINE 5-CARBOXYLATE REDUCTASE ISOFORM. [RefSeq;Acc:NM_013328] 0.131587 0.06503744 PYCR2
2.02856 887 KINESIN LIGHT CHAIN 2 (KLC 2). [SWISSPROT;Acc:Q9H0B6] 0.527178 0.259877943 KLC2
2.02876 1747 VACUOLAR ATP SYNTHASE SUBUNIT E (EC 3.6.3.14) (V-ATPASE E SUBUNIT) (VACUOLAR PROTON PUMP E SUBUNIT) (V-ATPASE 31 KDA SUBUNIT) (P31). [SWISSPROT;Acc:P36543] 0.480242 0.236717009 ATP6V1E1
2.02915 85 TRANSCRIPTION FACTOR DP-1 (E2F DIMERIZATION PARTNER 1) (DRTF1- POLYPEPTIDE-1) (DRTF1). [SWISSPROT;Acc:Q14186] 0.788778 0.388723357 no value
2.03821 2028 DENSITY-REGULATED PROTEIN (DRP) (DRP1 PROTEIN) (SMOOTH MUSCLE CELL ASSOCIATED PROTEIN-3) (SMAP-3). [SWISSPROT;Acc:O43583] 0.469395 0.230297663 DENR
2.0418 2447 HISTIDYL-TRNA SYNTHETASE HOMOLOG (EC 6.1.1.21) (HISTIDINE--TRNA LIGASE HOMOLOG) (HISRS). [SWISSPROT;Acc:P49590] 0.443267 0.21709619 HARS2
2.04196 2985 "BETA-ARRESTIN 1 (ARRESTIN, BETA 1). [SWISSPROT;Acc:P49407]" 0.282189 0.138195165 ARRB1
2.04623 2947 "6-PHOSPHOFRUCTOKINASE, LIVER TYPE (EC 2.7.1.11) (PHOSPHOFRUCTOKINASE 1) (PHOSPHOHEXOKINASE) (PHOSPHOFRUCTO-1-KINASE ISOZYME B) (PFK-B). [SWISSPROT;Acc:P17858]" 0.310225 0.151608079 PFKL
2.04792 678 TUBULIN TYROSINE LIGASE-LIKE PROTEIN HOTTL (HQP0207). [SWISSPROT;Acc:Q9Y4R7] 0.544593 0.265924938 BRPF1
2.05361 499 SEVEN IN ABSENTIA HOMOLOG 1. [RefSeq;Acc:NM_003031] 0.563143 0.274221006 no value
2.05735 3125 PALMITOYL-PROTEIN THIOESTERASE 2 PRECURSOR (EC 3.1.2.22) (PALMITOYL- PROTEIN HYDROLASE 2) (PPT-2) (G14). [SWISSPROT;Acc:Q9UMR5] 0.155614 0.075638078 EGFL8
2.05907 2034 0.473995 0.230198585 PUS3
2.06115 2033 TRNA PSEUDOURIDINE SYNTHASE A (EC 4.2.1.70) (PSEUDOURIDYLATE SYNTHASE I) (PSEUDOURIDINE SYNTHASE I) (URACIL HYDROLYASE). [SWISSPROT;Acc:Q9Y606] 0.474475 0.230199161 PUS1
2.06166 2993 MRNA DECAPPING ENZYME; HISTIDINE TRIAD PROTEIN MEMBER 5; HEAT SHOCK-LIKE PROTEIN 1. [RefSeq;Acc:NM_014026] 0.279017 0.135336088 DCPS
2.06448 628 SESTRIN 2 (HI95). [SWISSPROT;Acc:P58004] 0.553815 0.268258835 SESN2
2.06452 3016 COATOMER GAMMA SUBUNIT (GAMMA-COAT PROTEIN) (GAMMA-COP). [SWISSPROT;Acc:Q9Y678] 0.250617 0.121392382 COPG
2.07226 2948 "6-PHOSPHOFRUCTOKINASE, MUSCLE TYPE (EC 2.7.1.11) (PHOSPHOFRUCTOKINASE 1) (PHOSPHOHEXOKINASE) (PHOSPHOFRUCTO-1-KINASE ISOZYME A) (PFK-A) (PHOSPHOFRUCTOKINASE-M). [SWISSPROT;Acc:P08237]" 0.314149 0.15159729 PFKM
2.07581 2062 26S PROTEASE REGULATORY SUBUNIT 8 (PROTEASOME SUBUNIT P45) (THYROID HORMONE RECEPTOR INTERACTING PROTEIN 1) (TRIP1) (MSUG1 PROTEIN) (TAT-BINDING PROTEIN HOMOLOG 10) (TBP10) (P45/SUG). [SWISSPROT;Acc:P47210] 0.476629 0.229611092 PSMC5
2.0779 1384 UBIQUILIN 1 ISOFORM 1. [RefSeq;Acc:NM_013438] 0.508151 0.244550267 UBQLN1
2.08123 2883 NY-REN-24 ANTIGEN (FRAGMENT). [SPTREMBL;Acc:Q9Y5A4] 0.383948 0.184481292 C19orf29
2.08327 1589 HIV-1 REV BINDING PROTEIN 2; REV INTERACTING PROTEIN. [RefSeq;Acc:NM_007043] 0.501293 0.240627955 KRR1
2.08449 2011 PUTATIVE NUCLEOSIDE DIPHOSPHATE KINASE (EC 2.7.4.6) (NDK) (NDP KINASE). [SWISSPROT;Acc:O60361] 0.480816 0.230663616 NME2P1
2.0867 2084 40S RIBOSOMAL PROTEIN S29. [SWISSPROT;Acc:P30054] 0.477897 0.229020463 no value
2.09213 578 0.565201 0.270155774 IRF2BP2
2.09375 758 43 KDA RECEPTOR-ASSOCIATED PROTEIN OF THE SYNAPSE (RAPSYN) (ACETYLCHOLINE RECEPTOR-ASSOCIATED 43 KDA PROTEIN) (43 KDA POSTSYNAPTIC PROTEIN). [SWISSPROT;Acc:Q13702] 0.552551 0.263904955 RAPSN
2.10021 1282 CYSTEINE-RICH MOTOR NEURON 1; CYSTEINE-RICH REPEAT-CONTAINING PROTEIN S52 PRECURSOR. [RefSeq;Acc:NM_016441] 0.516861 0.246099676 CRIM1
2.1027 3132 PYRROLINE-5-CARBOXYLATE REDUCTASE (EC 1.5.1.2) (P5CR) (P5C REDUCTASE). [SWISSPROT;Acc:P32322] 0.137845 0.06555619 PYCR1
2.1041 1985 "28S RIBOSOMAL PROTEIN S12, MITOCHONDRIAL PRECURSOR (MPR-S12) (MT- RPS12). [SWISSPROT;Acc:O15235]" 0.485913 0.230936267 MRPS12
1986 40S RIBOSOMAL PROTEIN S23. [SWISSPROT;Acc:P39028] RPS23
2.10446 2684 POLY(A) POLYMERASE ALPHA (EC 2.7.7.19) (PAP) (POLYNUCLEOTIDE ADENYLYLTRANSFERASE ALPHA) (FRAGMENT). [SWISSPROT;Acc:P51003] 0.438432 0.20833468 PAPOLA
2.1077 1315 HYDROXYACID OXIDASE 1 (EC 1.1.3.15) (HAOX1) (GLYCOLATE OXIDASE) (GOX). [SWISSPROT;Acc:Q9UJM8] 0.517862 0.245700052 HAO1
2.10824 1317 ATP-DEPENDENT RNA HELICASE MGC2835; ATP-DEPENDENT RNA HELICASE; APOPTOSIS RELATED PROTEIN APR-5; DEAD BOX HELICASE 97 KDA. [RefSeq;Acc:NM_024072] 0.517911 0.245660361 DDX54
2.10953 1507 0.511781 0.242604277 NOC4L
1508 PROBABLE RIBOSOME BIOGENESIS PROTEIN NEP1 (C2F PROTEIN). [SWISSPROT;Acc:Q92979] EMG1
2.11039 1348 J KAPPA-RECOMBINATION SIGNAL BINDING PROTEIN (RBP-J KAPPA). [SWISSPROT;Acc:Q06330] 0.517438 0.245185961 RBPJ
2.11091 2754 ELECTRON TRANSFER FLAVOPROTEIN BETA-SUBUNIT (BETA-ETF). [SWISSPROT;Acc:P38117] 0.429899 0.203655769 ETFB

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/