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 measured Gene expected Rank description final
Results: HTML CSV LaTeX Showing element 2108 to 2157 of 3206 in total
Hugo
measured
expected
Rank
description
final
PAPOLG 0.377523 1.81111 2680 POLY(A) POLYMERASE GAMMA (EC 2.7.7.19) (PAP GAMMA) (POLYNUCLEOTIDE ADENYLYLTRANSFERASE GAMMA) (SRP RNA 3' ADENYLATING ENZYME). [SWISSPROT;Acc:Q9BWT3] 0.20844841
PAPSS1 0.0187206 0.0807026 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 0.231970222
PARD6G 0.0503166 0.239646 2649 PARTITIONING DEFECTIVE-6 HOMOLOG GAMMA (PAR-6 GAMMA) (PAR6D). [SWISSPROT;Acc:Q9BYG4] 0.209962194
PARK2 0.0372023 0.196899 2864 "PARKINSON DISEASE (AUTOSOMAL RECESSIVE, JUVENILE) 2, PARKIN ISOFORM 1; PARKIN. [RefSeq;Acc:NM_004562]" 0.188941031
PARL 0.177185 0.702909 1080 PRESENILINS ASSOCIATED RHOMBOID-LIKE PROTEIN. [RefSeq;Acc:NM_018622] 0.252073882
PARS2 0.205001 0.946559 2477 SIMILAR TO TRNA SYNTHETASE CLASS II. [RefSeq;Acc:NM_152268] 0.216574984
PASK 0.0869475 0.328537 736 PAS DOMAIN CONTAINING SERINE/THREONINE KINASE; PAS-SERINE/THREONINE KINASE. [RefSeq;Acc:NM_015148] 0.264650557
PAX6 0.876793 3.36108 836 "PAIRED BOX PROTEIN PAX-6 (OCULORHOMBIN) (ANIRIDIA, TYPE II PROTEIN). [SWISSPROT;Acc:P26367]" 0.260866448
PBK 0.0544673 0.15506 152 T-LAK CELL-ORIGINATED PROTEIN KINASE; SPERMATOGENESIS-RELATED PROTEIN KINASE; PDZ-BINDING KINASE; PBK; MAPKK-LIKE PROTEIN KINASE; SERINE/THREONINE PROTEIN KINASE. [RefSeq;Acc:NM_018492] 0.351265962
PBLD 0.0230825 0.11461 2771 MAWD BINDING PROTEIN (UNKNOWN PROTEIN 32 FROM 2D-PAGE OF LIVER TISSUE). [SWISSPROT;Acc:P30039] 0.201400401
PBRM1 0.128218 0.517633 1233 POLYBROMO 1. [RefSeq;Acc:NM_018165] 0.247700591
PBX1 0.301322 1.19272 1069 PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR-1 (HOMEOBOX PROTEIN PBX1) (HOMEOBOX PROTEIN PRL). [SWISSPROT;Acc:P40424] 0.252634315
PBX3 0.283637 1.12271 1063 PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR-3 (HOMEOBOX PROTEIN PBX3). [SWISSPROT;Acc:P40426] 0.252636032
PBX4 0.122601 0.485287 1062 PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR 4. [RefSeq;Acc:NM_025245] 0.252636069
PC 0.223983 1.30736 2918 "PYRUVATE CARBOXYLASE, MITOCHONDRIAL PRECURSOR (EC 6.4.1.1) (PYRUVIC CARBOXYLASE) (PCB). [SWISSPROT;Acc:P11498]" 0.171324654
PCAF 0.162045 0.742662 2420 P300/CBP-ASSOCIATED FACTOR (EC 2.3.1.-) (P/CAF) (HISTONE ACETYLASE PCAF). [SWISSPROT;Acc:Q92831] 0.218194818
PCCB 0.114033 0.45456 1109 "PROPIONYL-COA CARBOXYLASE BETA CHAIN, MITOCHONDRIAL PRECURSOR (EC 6.4.1.3) (PCCASE BETA SUBUNIT) (PROPANOYL-COA:CARBON DIOXIDE LIGASE BETA SUBUNIT). [SWISSPROT;Acc:P05166]" 0.250864572
PCDH15 0.0344025 0.156164 2358 PROTOCADHERIN 15 PRECURSOR. [SWISSPROT;Acc:Q96QU1] 0.220297252
PCF11 0.251152 1.15996 2479 PRE-MRNA CLEAVAGE COMPLEX II PROTEIN PCF11 (FRAGMENT). [SWISSPROT;Acc:O94913] 0.216517811
PCID2 0.0315995 0.129562 1422 0.243894815
PCNA 0.754507 3.65293 2722 PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA) (CYCLIN). [SWISSPROT;Acc:P12004] 0.206548442
PCSK5 0.0398596 0.408247 3086 PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 5 PRECURSOR (EC 3.4.21.-) (PROPROTEIN CONVERTASE PC5) (SUBTILISIN/KEXIN-LIKE PROTEASE PC5) (CONVERTASE PC5) (PC6) (HPC6). [SWISSPROT;Acc:Q92824] 0.09763599
PCYT1A 0.0187206 0.0807026 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] 0.231970222
PCYT1B 0.0164226 0.0707964 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] 0.231969422
PCYT2 0.278946 1.06742 816 ETHANOLAMINE-PHOSPHATE CYTIDYLYLTRANSFERASE (EC 2.7.7.14) (PHOSPHORYLETHANOLAMINE TRANSFERASE) (CTP:PHOSPHOETHANOLAMINE CYTIDYLYLTRANSFERASE). [SWISSPROT;Acc:Q99447] 0.261327313
PDC 0.0280767 0.11112 1058 PHOSDUCIN (PHD) (33 KDA PHOTOTRANSDUCING PROTEIN) (MEKA PROTEIN). [SWISSPROT;Acc:P20941] 0.252670086
PDCD11 0.132484 0.570026 1901 RRP5 PROTEIN HOMOLOG (PROGRAMMED CELL DEATH PROTEIN 11). [SWISSPROT;Acc:Q14690] 0.232417469
PDCD5 0.218499 0.930463 1796 PROGRAMMED CELL DEATH PROTEIN 5 (TFAR19 PROTEIN) (TF-1 CELL APOPTOSIS RELATED GENE-19 PROTEIN). [SWISSPROT;Acc:O14737] 0.234828252
PDCD6 0.182783 0.506093 114 PROGRAMMED CELL DEATH PROTEIN 6 (PROBABLE CALCIUM-BINDING PROTEIN ALG- 2). [SWISSPROT;Acc:O75340] 0.361164845
PDCL 0.0344183 0.136218 1054 PHOSDUCIN-LIKE PROTEIN (PHLP). [SWISSPROT;Acc:Q13371] 0.252670719
PDHA1 0.38076 1.65321 2025 "PYRUVATE DEHYDROGENASE E1 COMPONENT ALPHA SUBUNIT, SOMATIC FORM, MITOCHONDRIAL PRECURSOR (EC 1.2.4.1) (PDHE1-A TYPE I). [SWISSPROT;Acc:P08559]" 0.230315568
PDHA2 0.353795 1.53626 2030 "PYRUVATE DEHYDROGENASE E1 COMPONENT ALPHA SUBUNIT, TESTIS-SPECIFIC FORM, MITOCHONDRIAL PRECURSOR (EC 1.2.4.1) (PDHE1-A TYPE II). [SWISSPROT;Acc:P29803]" 0.230296304
PDHB 0.804341 3.6465 2345 "PYRUVATE DEHYDROGENASE E1 COMPONENT BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.2.4.1) (PDHE1-B). [SWISSPROT;Acc:P11177]" 0.220578911
PDK1 0.844424 3.93515 2550 "[PYRUVATE DEHYDROGENASE [LIPOAMIDE]] KINASE ISOZYME 1, MITOCHONDRIAL PRECURSOR (EC 2.7.1.99) (PYRUVATE DEHYDROGENASE KINASE ISOFORM 1). [SWISSPROT;Acc:Q15118]" 0.214584959
PDK2 0.845658 3.9409 2549 "[PYRUVATE DEHYDROGENASE [LIPOAMIDE]] KINASE ISOZYME 2, MITOCHONDRIAL PRECURSOR (EC 2.7.1.99) (PYRUVATE DEHYDROGENASE KINASE ISOFORM 2). [SWISSPROT;Acc:Q15119]" 0.214584993
PDLIM5 1.83106 6.64504 466 LIM PROTEIN (SIMILAR TO RAT PROTEIN KINASE C-BINDING ENIGMA); ENIGMA HOMOLOG. [RefSeq;Acc:NM_006457] 0.275552894
PDPK1 0.61809 3.46554 2891 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 (EC 2.7.1.37) (HPDK1). [SWISSPROT;Acc:O15530] 0.178353157
PDRG1 0.129986 0.53787 1551 0.241668061
PDSS1 0.294256 1.3369 2369 TRANS-PRENYLTRANSFERASE; POLYPRENYL PYROPHOSPHATE SYNTHETASE. [RefSeq;Acc:NM_014317] 0.220103224
PDXDC1 0.306813 0.87318 145 SIMILAR TO EXPRESSED SEQUENCE AA415817. [SPTREMBL;Acc:Q8N4Q9] 0.351374287
PEF1 0.318787 0.941277 172 PEF PROTEIN WITH A LONG N-TERMINAL HYDROPHOBIC DOMAIN (PEFLIN). [RefSeq;Acc:NM_012392] 0.338675013
PEO1 0.176631 0.678587 861 TWINKLE; LIKELY ORTHOLOG OF MOUSE T7 GP4-LIKE PROTEIN WITH INTRAMITOCHONDRIAL NUCLEOID LOCALIZATION. [RefSeq;Acc:NM_021830] 0.260292343
PERLD1 0.0366052 0.143236 970 CAB2. [RefSeq;Acc:NM_033419] 0.255558658
PES1 0.913889 3.68475 1220 PESCADILLO HOMOLOG 1. [SWISSPROT;Acc:O00541] 0.248019269
PET112L 0.0946707 0.399507 1740 "PROBABLE GLUTAMYL-TRNA(GLN) AMIDOTRANSFERASE SUBUNIT B, MITOCHONDRIAL PRECURSOR (EC 6.3.5.-) (GLU-ADT SUBUNIT B) (CYTOCHROME OXIDASE ASSEMBLY FACTOR PET112 HOMOLOG). [SWISSPROT;Acc:O75879]" 0.236968814
PEX1 0.0194686 0.0842002 1964 PEROXISOME BIOGENESIS FACTOR 1 (PEROXIN-1) (PEROXISOME BIOGENESIS DISORDER PROTEIN 1). [SWISSPROT;Acc:O43933] 0.231217978
PEX14 0.500223 1.91396 815 PEROXISOMAL MEMBRANE PROTEIN PEX14 (PEROXIN-14) (PEROXISOMAL MEMBRANE ANCHOR PROTEIN PEX14) (PTS1 RECEPTOR DOCKING PROTEIN). [SWISSPROT;Acc:O75381] 0.261354992
PEX19 0.245859 0.88087 383 PEROXISOMAL FARNESYLATED PROTEIN (33 KDA HOUSEKEEPING PROTEIN) (PEROXIN 19). [SWISSPROT;Acc:P40855] 0.27910929
PEX5 1.42729 3.51439 67 PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR (PEROXISMORE RECEPTOR 1) (PEROXISOMAL C-TERMINAL TARGETING SIGNAL IMPORT RECEPTOR) (PTS1-BP) (PEROXIN-5) (PTS1 RECEPTOR). [SWISSPROT;Acc:P50542] 0.406127379
PEX5L 0.253658 0.812851 248 PXR2B PROTEIN. [RefSeq;Acc:NM_016559] 0.312059652

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/