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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Hugo Gene measured expected Rank description final
Results: HTML CSV LaTeX Showing element 2158 to 2207 of 3206 in total
Hugo
measured
expected
Rank
description
final
PEX7 0.141529 0.715904 2808 PEROXISOMAL TARGETING SIGNAL 2 RECEPTOR (PTS2 RECEPTOR) (PEROXIN-7). [SWISSPROT;Acc:O00628] 0.197692707
PFAS 0.100408 0.416 1554 PHOSPHORIBOSYLFORMYLGLYCINAMIDINE SYNTHASE (EC 6.3.5.3) (FGAM SYNTHASE) (FGAMS) (FORMYLGLYCINAMIDE RIBOTIDE AMIDOTRANSFERASE) (FGARAT) (FORMYLGLYCINAMIDE RIBOTIDE SYNTHETASE). [SWISSPROT;Acc:O15067] 0.241365385
PFDN1 0.128438 0.480838 661 PREFOLDIN SUBUNIT 1. [SWISSPROT;Acc:O60925] 0.267112832
PFDN2 0.15115 0.643016 1789 PREFOLDIN SUBUNIT 2 (HSPC231). [SWISSPROT;Acc:Q9UHV9] 0.235064135
PFDN5 0.299475 1.30706 2076 PREFOLDIN SUBUNIT 5 (C-MYC BINDING PROTEIN MM-1) (MYC MODULATOR 1). [SWISSPROT;Acc:Q99471] 0.229121081
PFKL 0.310225 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]" 0.151608079
PFKM 0.314149 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]" 0.15159729
PFKP 0.367121 2.42367 2949 "6-PHOSPHOFRUCTOKINASE, TYPE C (EC 2.7.1.11) (PHOSPHOFRUCTOKINASE 1) (PHOSPHOHEXOKINASE) (PHOSPHOFRUCTO-1-KINASE ISOZYME C) (PFK-C) (6-PHOSPHOFRUCTOKINASE, PLATELET TYPE). [SWISSPROT;Acc:Q01813]" 0.151473179
PGAM2 0.0270059 0.10746 1096 PHOSPHOGLYCERATE MUTASE 2 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13) (PHOSPHOGLYCERATE MUTASE ISOZYME M) (PGAM-M) (BPG-DEPENDENT PGAM 2) (MUSCLE-SPECIFIC PHOSPHOGLYCERATE MUTASE). [SWISSPROT;Acc:P15259] 0.251311186
PGAM4 0.030826 0.122661 1097 PUTATIVE PHOSPHOGLYCERATE MUTASE 3 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13). [SWISSPROT;Acc:Q8N0Y7] 0.251310522
PGAM5 0.099187 0.486671 2753 0.203807089
PGC 0.0442218 0.200737 2359 GASTRICSIN PRECURSOR (EC 3.4.23.3) (PEPSINOGEN C). [SWISSPROT;Acc:P20142] 0.220297205
PGD 0.0670488 0.303687 2339 "6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING (EC 1.1.1.44). [SWISSPROT;Acc:P52209]" 0.220782582
PGGT1B 0.0378747 0.146984 926 GERANYLGERANYL TRANSFERASE TYPE I BETA SUBUNIT (EC 2.5.1.-) (TYPE I PROTEIN GERANYL-GERANYLTRANSFERASE BETA SUBUNIT) (GGTASE-I-BETA). [SWISSPROT;Acc:P53609] 0.257679067
PGK1 0.286165 1.2723 2215 PHOSPHOGLYCERATE KINASE 1 (EC 2.7.2.3) (PRIMER RECOGNITION PROTEIN 2) (PRP 2). [SWISSPROT;Acc:P00558] 0.224919437
PGK2 0.265015 1.17827 2217 "PHOSPHOGLYCERATE KINASE, TESTIS SPECIFIC (EC 2.7.2.3). [SWISSPROT;Acc:P07205]" 0.224918737
PGLS 0.0750119 0.345603 2449 6-PHOSPHOGLUCONOLACTONASE (EC 3.1.1.31) (6PGL). [SWISSPROT;Acc:O95336] 0.217046438
PGM2 0.460943 1.71147 593 0.269325784
PGM2L1 0.393043 1.45917 589 0.269360664
PGM3 0.537765 1.99671 594 PHOSPHOACETYLGLUCOSAMINE MUTASE (EC 5.4.2.3) (PAGM) (ACETYLGLUCOSAMINE PHOSPHOMUTASE) (N-ACETYLGLUCOSAMINE-PHOSPHATE MUTASE) (PHOSPHOGLUCOMUTASE 3). [SWISSPROT;Acc:O95394] 0.269325541
PHB 0.26817 1.22481 2403 PROHIBITIN. [SWISSPROT;Acc:P35232] 0.218948245
PHGDH 0.489733 2.24292 2418 D-3-PHOSPHOGLYCERATE DEHYDROGENASE (EC 1.1.1.95) (3-PGDH). [SWISSPROT;Acc:O43175] 0.218346174
PHLPP 0.167352 0.699345 1631 0.2392982
PHLPPL 0.132038 0.551746 1630 0.239309392
PICALM 0.276961 0.998529 428 PHOSPHATIDYLINOSITOL-BINDING CLATHRIN ASSEMBLY PROTEIN (CLATHRIN ASSEMBLY LYMPHOID MYELOID LEUKEMIA PROTEIN). [SWISSPROT;Acc:Q13492] 0.27736901
PIH1D1 0.311796 1.27783 1413 0.244004289
PIH1D2 0.0640044 0.290417 2349 0.220387925
PIK3C2A 0.0345092 0.132688 881 "PHOSPHOINOSITIDE-3-KINASE, CLASS 2, ALPHA POLYPEPTIDE; C2-CONTAINING PHOSPHATIDYLINOSITOL KINASE. [RefSeq;Acc:NM_002645]" 0.260077776
PIK3C2B 0.0265832 0.102213 883 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] 0.260076507
PIK3C2G 0.0242456 0.0932247 882 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] 0.260076997
PIK3R1 0.0593799 0.266211 2256 PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY ALPHA SUBUNIT (PI3-KINASE P85-ALPHA SUBUNIT) (PTDINS-3-KINASE P85-ALPHA) (PI3K). [SWISSPROT;Acc:P27986] 0.223055772
PIK3R2 0.0560483 0.251275 2258 PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY BETA SUBUNIT (PI3-KINASE P85-BETA SUBUNIT) (PTDINS-3-KINASE P85-BETA). [SWISSPROT;Acc:O00459] 0.223055616
PIK3R3 0.0597741 0.267978 2253 PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY GAMMA SUBUNIT (PI3-KINASE P85-GAMMA SUBUNIT) (PTDINS-3-KINASE P85-GAMMA) (P55PIK). [SWISSPROT;Acc:Q92569] 0.223055997
PIN1 0.347798 1.52661 2139 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1 (EC 5.2.1.8) (ROTAMASE PIN1) (PPIASE PIN1). [SWISSPROT;Acc:Q13526] 0.22782374
PITRM1 0.0574917 0.781248 3127 METALLOPROTEASE 1; METALLOPROTEASE 1 (PITRILYSIN FAMILY). [RefSeq;Acc:NM_014889] 0.073589564
PKM2 0.184777 1.05445 2894 "PYRUVATE KINASE, M1 ISOZYME (EC 2.7.1.40) (PYRUVATE KINASE MUSCLE ISOZYME) (CYTOSOLIC THYROID HORMONE-BINDING PROTEIN) (CTHBP) (THBP1). [SWISSPROT;Acc:P14618]" 0.175235431
PLD1 0.177815 0.816721 2429 PHOSPHOLIPASE D1 (EC 3.1.4.4) (PLD 1) (CHOLINE PHOSPHATASE 1) (PHOSPHATIDYLCHOLINE-HYDROLYZING PHOSPHOLIPASE D1) (HPLD1). [SWISSPROT;Acc:Q13393] 0.217718168
PLD2 0.146403 0.672152 2428 PHOSPHOLIPASE D2 (EC 3.1.4.4) (PLD 2) (CHOLINE PHOSPHATASE 2) (PHOSPHATIDYLCHOLINE-HYDROLYZING PHOSPHOLIPASE D2) (PLD1C) (HPLD2). [SWISSPROT;Acc:O14939] 0.21781234
PLDN 0.153744 0.559309 470 "PALLIDIN; PALLID (MOUSE) HOMOLOG, PALLIDIN. [RefSeq;Acc:NM_012388]" 0.274882042
PLEKHC1 0.0405241 0.188688 2506 "PLECKSTRIN HOMOLOGY DOMAIN CONTAINING, FAMILY C (WITH FERM DOMAIN) MEMBER 1; MITOGEN INDUCIBLE 2; KINDLIN 2. [RefSeq;Acc:NM_006832]" 0.214767765
PLEKHF2 0.2305 0.916205 1090 PHAFIN 2; PH AND FYVE DOMAIN-CONTAINING PROTEIN 2. [RefSeq;Acc:NM_024613] 0.251581251
PLEKHG2 0.024304 0.139564 2905 0.174142329
PLEKHG6 0.113929 0.295729 87 0.38524798
PLK1 0.170317 0.640229 677 SERINE/THREONINE-PROTEIN KINASE PLK (EC 2.7.1.-) (PLK-1) (SERINE- THREONINE PROTEIN KINASE 13) (STPK13). [SWISSPROT;Acc:P53350] 0.266025125
PLRG1 0.709304 2.4753 326 "PLEIOTROPIC REGULATOR 1 (PRL1HOMOLOG, ARABIDOPSIS); PLEIOTROPIC REGULATOR 1 (PRL1, ARABIDOPSIS HOMOLOG). [RefSeq;Acc:NM_002669]" 0.286552741
PLSCR2 0.252989 1.00989 1130 PHOSPHOLIPID SCRAMBLASE 2 (PL SCRAMBLASE 2) (CA(2+)-DEPENDENT PHOSPHOLIPID SCRAMBLASE 2). [SWISSPROT;Acc:Q9NRY7] 0.250511442
PLSCR4 0.198834 0.793992 1137 PHOSPHOLIPID SCRAMBLASE 4 (PL SCRAMBLASE 4) (CA(2+)-DEPENDENT PHOSPHOLIPID SCRAMBLASE 4). [SWISSPROT;Acc:Q9NRQ2] 0.250423178
PLTP 0.0139025 0.0611788 2163 PHOSPHOLIPID TRANSFER PROTEIN PRECURSOR (LIPID TRANSFER PROTEIN II). [SWISSPROT;Acc:P55058] 0.227243751
PMM1 0.146657 0.660778 2317 PHOSPHOMANNOMUTASE 1 (EC 5.4.2.8) (PMM 1) (PMMH-22). [SWISSPROT;Acc:Q92871] 0.221945949
PMM2 0.18235 0.82204 2318 PHOSPHOMANNOMUTASE 2 (EC 5.4.2.8) (PMM 2). [SWISSPROT;Acc:O15305] 0.221826189

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/