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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Gene description Rank measured expected final Hugo
Results: HTML CSV LaTeX Showing element 2301 to 2350 of 3206 in total
description
Rank
measured
expected
final
Hugo
PALMITOYL-PROTEIN THIOESTERASE 1 PRECURSOR (EC 3.1.2.22) (PALMITOYL- PROTEIN HYDROLASE 1). [SWISSPROT;Acc:P50897] 795 0.0690966 0.263715 0.2620124 PPT1
PALMITOYL-PROTEIN THIOESTERASE 2 PRECURSOR (EC 3.1.2.22) (PALMITOYL- PROTEIN HYDROLASE 2) (PPT-2) (G14). [SWISSPROT;Acc:Q9UMR5] 3125 0.155614 2.05735 0.075638078 EGFL8
PANTOTHENATE KINASE 1 (EC 2.7.1.33) (PANTOTHENIC ACID KINASE 1) (HPANK1) (HPANK). [SWISSPROT;Acc:Q8TE04] 3038 0.0241982 0.22041 0.109787215 PANK1
PANTOTHENATE KINASE 3 (EC 2.7.1.33) (PANTOTHENIC ACID KINASE 3) (HPANK3). [SWISSPROT;Acc:Q9H999] 3040 0.0191226 0.174179 0.109787058 PANK3
PARAFIBROMIN. [RefSeq;Acc:NM_024529] 1118 0.116454 0.464305 0.250813582 CDC73
PARASPECKLE PROTEIN 1. [RefSeq;Acc:NM_018282] 1675 0.203402 0.853581 0.238292558 PSPC1
PARTITIONING DEFECTIVE-6 HOMOLOG GAMMA (PAR-6 GAMMA) (PAR6D). [SWISSPROT;Acc:Q9BYG4] 2649 0.0503166 0.239646 0.209962194 PARD6G
PAS DOMAIN CONTAINING SERINE/THREONINE KINASE; PAS-SERINE/THREONINE KINASE. [RefSeq;Acc:NM_015148] 736 0.0869475 0.328537 0.264650557 PASK
PAXILLIN. [SWISSPROT;Acc:P49023] 198 0.183967 0.570423 0.322509787 PXN
PBK1 PROTEIN. [SPTREMBL;Acc:O76021] 1505 0.485772 2.00168 0.242682147 RSL1D1
PC4 AND SFRS1 INTERACTING PROTEIN 2; PC4 AND SFRS1 INTERACTING PROTEIN 1; TRANSCRIPTIONAL COACTIVATOR P52/P75. [RefSeq;Acc:NM_033222] 2869 0.0308872 0.163476 0.188940273 PSIP1
PDZ/COILED-COIL DOMAIN BINDING PARTNER FOR THE RHO-FAMILY GTPASE TC10; FUSED IN GLIOBLASTOMA; GOLGI ASSOCIATED PDZ AND COILED-COIL MOTIF CONTAINING PROTEIN; CFTR-ASSOCIATED LIGAND. [RefSeq;Acc:NM_020399] 961 0.909945 3.55389 0.256041971 GOPC
PEF PROTEIN WITH A LONG N-TERMINAL HYDROPHOBIC DOMAIN (PEFLIN). [RefSeq;Acc:NM_012392] 172 0.318787 0.941277 0.338675013 PEF1
PEPSIN A PRECURSOR (EC 3.4.23.1). [SWISSPROT;Acc:P00790] 2366 0.0604093 0.274218 0.220296625 no value
PEPTIDE METHIONINE SULFOXIDE REDUCTASE (EC 1.8.4.6) (PROTEIN- METHIONINE-S-OXIDE REDUCTASE) (PEPTIDE MET(O) REDUCTASE). [SWISSPROT;Acc:Q9UJ68] 2224 0.0281672 0.125329 0.224746068 MSRA
PEPTIDYL PROLYL ISOMERASE H; CYCLOPHILIN H. [RefSeq;Acc:NM_006347] 1887 0.039427 0.1694 0.232744982 PPIH
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE B PRECURSOR (EC 5.2.1.8) (PPIASE) (ROTAMASE) (CYCLOPHILIN B) (S-CYCLOPHILIN) (SCYLP) (CYP-S1). [SWISSPROT;Acc:P23284] 2100 0.0360136 0.15771 0.228353307 PPIB
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E (EC 5.2.1.8) (PPIASE E) (ROTAMASE E) (CYCLOPHILIN E) (CYCLOPHILIN 33). [SWISSPROT;Acc:Q9UNP9] 3018 0.0424091 0.349357 0.121391871 PPIE
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1 (EC 5.2.1.8) (ROTAMASE PIN1) (PPIASE PIN1). [SWISSPROT;Acc:Q13526] 2139 0.347798 1.52661 0.22782374 PIN1
PEPTIDYLPROLYL ISOMERASE-LIKE 4; CYCLOPHILIN-TYPE PEPTIDYL-PROLYL CIS-TRANS ISOMERASE; PPIASE; SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR-18. [RefSeq;Acc:NM_139126] 904 0.227308 0.879442 0.258468438 PPIL4
PERIPHERAL PLASMA MEMBRANE PROTEIN CASK (EC 2.7.1.-) (HCASK) (CALCIUM/CALMODULIN-DEPENDENT SERINE PROTEIN KINASE) (LIN-2 HOMOLOG). [SWISSPROT;Acc:O14936] 1269 0.685788 2.77992 0.24669343 CASK
PEROXIREDOXIN 4 (EC 1.11.1.-) (PRX-IV) (THIOREDOXIN PEROXIDASE AO372) (THIOREDOXIN-DEPENDENT PEROXIDE REDUCTASE A0372) (ANTIOXIDANT ENZYME AOE372) (AOE37-2). [SWISSPROT;Acc:Q13162] 328 0.0946713 0.331704 0.285408979 PRDX4
PEROXISOMAL ACYL-COA THIOESTERASE 2B; LIKELY ORTHOLOG OF MOUSE PEROXISOMAL ACYL-COA THIOESTERASE 2B. [RefSeq;Acc:NM_152331] 577 0.257341 0.951909 0.270342018 ACOT4
PEROXISOMAL ACYL-COENZYME A THIOESTER HYDROLASE 2A (EC 3.1.2.2) (PEROXISOMAL LONG-CHAIN ACYL-COA THIOESTERASE 2) (ZAP128). [SWISSPROT;Acc:P49753] 576 0.230682 0.853273 0.270349583 ACOT1
PEROXISOMAL CARNITINE OCTANOYLTRANSFERASE (EC 2.3.1.-) (COT). [SWISSPROT;Acc:Q9UKG9] 739 0.117061 0.442554 0.264512353 CROT
PEROXISOMAL FARNESYLATED PROTEIN (33 KDA HOUSEKEEPING PROTEIN) (PEROXIN 19). [SWISSPROT;Acc:P40855] 383 0.245859 0.88087 0.27910929 PEX19
PEROXISOMAL MEMBRANE PROTEIN 2 (22 KDA PEROXISOMAL MEMBRANE PROTEIN). [SWISSPROT;Acc:Q9NR77] 1769 0.0420153 0.178036 0.235993282 PXMP2
PEROXISOMAL MEMBRANE PROTEIN PEX14 (PEROXIN-14) (PEROXISOMAL MEMBRANE ANCHOR PROTEIN PEX14) (PTS1 RECEPTOR DOCKING PROTEIN). [SWISSPROT;Acc:O75381] 815 0.500223 1.91396 0.261354992 PEX14
PEROXISOMAL N1-ACETYL-SPERMINE/SPERMIDINE OXIDASE. [RefSeq;Acc:NM_152911] 443 0.0442587 0.15995 0.276703345 PAOX
PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR (PEROXISMORE RECEPTOR 1) (PEROXISOMAL C-TERMINAL TARGETING SIGNAL IMPORT RECEPTOR) (PTS1-BP) (PEROXIN-5) (PTS1 RECEPTOR). [SWISSPROT;Acc:P50542] 67 1.42729 3.51439 0.406127379 PEX5
PEROXISOMAL TARGETING SIGNAL 2 RECEPTOR (PTS2 RECEPTOR) (PEROXIN-7). [SWISSPROT;Acc:O00628] 2808 0.141529 0.715904 0.197692707 PEX7
PEROXISOME BIOGENESIS FACTOR 1 (PEROXIN-1) (PEROXISOME BIOGENESIS DISORDER PROTEIN 1). [SWISSPROT;Acc:O43933] 1964 0.0194686 0.0842002 0.231217978 PEX1
PESCADILLO HOMOLOG 1. [SWISSPROT;Acc:O00541] 1220 0.913889 3.68475 0.248019269 PES1
PHAFIN 2; PH AND FYVE DOMAIN-CONTAINING PROTEIN 2. [RefSeq;Acc:NM_024613] 1090 0.2305 0.916205 0.251581251 PLEKHF2
PHD FINGER PROTEIN 9. [RefSeq;Acc:NM_018062] 1077 0.0732296 0.290291 0.252262729 FANCL
PHENYLALANINE-4-HYDROXYLASE (EC 1.14.16.1) (PAH) (PHE-4- MONOOXYGENASE). [SWISSPROT;Acc:P00439] 209 1.48249 4.62476 0.320555013 PAH
PHENYLALANINE-TRNA SYNTHETASE. [RefSeq;Acc:NM_006567] 2787 0.0790566 0.39545 0.199915539 FARS2
PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN (EC 6.1.1.20) (PHENYLALANINE- -TRNA LIGASE ALPHA CHAIN) (PHERS) (CML33). [SWISSPROT;Acc:Q9Y285] 2786 FARSA
PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN (EC 6.1.1.20) (PHENYLALANINE-- TRNA LIGASE BETA CHAIN) (PHERS) (HSPC173). [SWISSPROT;Acc:Q9NSD9] 2781 0.0470468 0.234118 0.200953365 FARSB
PHENYLETHANOLAMINE N-METHYLTRANSFERASE (EC 2.1.1.28) (PNMTASE) (NORADRENALINE N-METHYLTRANSFERASE). [SWISSPROT;Acc:P11086] 293 0.0437393 0.144924 0.301808534 PNMT
PHOSDUCIN (PHD) (33 KDA PHOTOTRANSDUCING PROTEIN) (MEKA PROTEIN). [SWISSPROT;Acc:P20941] 1058 0.0280767 0.11112 0.252670086 PDC
PHOSDUCIN-LIKE PROTEIN (PHLP). [SWISSPROT;Acc:Q13371] 1054 0.0344183 0.136218 0.252670719 PDCL
PHOSPHATIDATE CYTIDYLYLTRANSFERASE 1 (EC 2.7.7.41) (CDP-DIGLYCERIDE SYNTHETASE 1) (CDP-DIGLYCERIDE PYROPHOSPHORYLASE 1) (CDP- DIACYLGLYCEROL SYNTHASE 1) (CDS 1) (CTP:PHOSPHATIDATE CYTIDYLYLTRANSFERASE 1) (CDP-DAG SYNTHASE 1) (CDP-DG SYNTHETASE 1). [Source 2661 0.558539 2.66089 0.209906836 CDS1
PHOSPHATIDATE CYTIDYLYLTRANSFERASE 2 (EC 2.7.7.41) (CDP-DIGLYCERIDE SYNTHETASE 2) (CDP-DIGLYCERIDE PYROPHOSPHORYLASE 2) (CDP- DIACYLGLYCEROL SYNTHASE 2) (CDS 2) (CTP:PHOSPHATIDATE CYTIDYLYLTRANSFERASE 2) (CDP-DAG SYNTHASE 2) (CDP-DG SYNTHETASE 2). [Source 2642 0.515928 2.45712 0.209972651 CDS2
PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY ALPHA SUBUNIT (PI3-KINASE P85-ALPHA SUBUNIT) (PTDINS-3-KINASE P85-ALPHA) (PI3K). [SWISSPROT;Acc:P27986] 2256 0.0593799 0.266211 0.223055772 PIK3R1
PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY BETA SUBUNIT (PI3-KINASE P85-BETA SUBUNIT) (PTDINS-3-KINASE P85-BETA). [SWISSPROT;Acc:O00459] 2258 0.0560483 0.251275 0.223055616 PIK3R2
PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY GAMMA SUBUNIT (PI3-KINASE P85-GAMMA SUBUNIT) (PTDINS-3-KINASE P85-GAMMA) (P55PIK). [SWISSPROT;Acc:Q92569] 2253 0.0597741 0.267978 0.223055997 PIK3R3
PHOSPHATIDYLINOSITOL-4-PHOSPHATE 3-KINASE C2 DOMAIN-CONTAINING BETA POLYPEPTIDE (EC 2.7.1.154) (PHOSPHOINOSITIDE 3-KINASE-C2-BETA) (PTDINS-3-KINASE C2 BETA) (PI3K-C2BETA) (C2-PI3K). [SWISSPROT;Acc:O00750] 883 0.0265832 0.102213 0.260076507 PIK3C2B
PHOSPHATIDYLINOSITOL-4-PHOSPHATE 3-KINASE C2 DOMAIN-CONTAINING GAMMA POLYPEPTIDE (EC 2.7.1.154) (PHOSPHOINOSITIDE 3-KINASE-C2-GAMMA) (PTDINS-3-KINASE C2 GAMMA) (PI3K-C2GAMMA). [SWISSPROT;Acc:O75747] 882 0.0242456 0.0932247 0.260076997 PIK3C2G
PHOSPHATIDYLINOSITOL-BINDING CLATHRIN ASSEMBLY PROTEIN (CLATHRIN ASSEMBLY LYMPHOID MYELOID LEUKEMIA PROTEIN). [SWISSPROT;Acc:Q13492] 428 0.276961 0.998529 0.27736901 PICALM

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/