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 2851 to 2900 of 3206 in total
Rank
description
measured
expected
final
Hugo
2851 "PROTEIN PHOSPHATASE 1, REGULATORY SUBUNIT 7; SDS22. [RefSeq;Acc:NM_002712]" 0.0699506 0.365592 0.19133515 PPP1R7
2852 SMALL GLUTAMINE RICH PROTEIN WITH TETRATRICOPEPTIDE REPEATS 2. [RefSeq;Acc:NM_019072] 0.839834 4.39067 0.191276958 no value
2853 "ISOCITRATE DEHYDROGENASE [NADP], MITOCHONDRIAL PRECURSOR (EC 1.1.1.42) (OXALOSUCCINATE DECARBOXYLASE) (IDH) (NADP+-SPECIFIC ICDH) (IDP) (ICD-M). [SWISSPROT;Acc:P48735]" 0.0716408 0.374722 0.191183864 IDH2
2854 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE DELTA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 4) (1-AGPAT 4) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-DELTA) (LPAAT-DELTA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 4). [SWISSPROT;Acc:Q9NRZ5] 0.24139 1.26323 0.191089509 AGPAT4
2855 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE GAMMA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 3) (1-AGPAT 3) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-GAMMA) (LPAAT-GAMMA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 3). [SWISSPROT;Acc:Q9NRZ7] 0.214138 1.12158 0.190925302 AGPAT3
2856 TRIOSEPHOSPHATE ISOMERASE (EC 5.3.1.1) (TIM). [SWISSPROT;Acc:P00938] 0.158456 0.830447 0.190808083 TPI1
2857 TRNA (5-METHYLAMINOMETHYL-2-THIOURIDYLATE)-METHYLTRANSFERASE (EC 2.1.1.61). [SWISSPROT;Acc:O75648] 0.0583389 0.30593 0.190693623 TRMU
2858 "TREHALASE PRECURSOR (EC 3.2.1.28) (ALPHA,ALPHA-TREHALASE) (ALPHA,ALPHA-TREHALOSE GLUCOHYDROLASE). [SWISSPROT;Acc:O43280]" 0.0811667 0.428605 0.189374132 TREH
2859 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE ALPHA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 1) (1-AGPAT 1) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-ALPHA) (LPAAT-ALPHA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 1) (G15 PROTEIN). [SWISSPROT;Acc:Q9 0.246538 1.30479 0.188948413 no value
2860 0.0307477 0.162737 0.188941052 ORAI1
2861 RW1 PROTEIN (FRAGMENT). [SWISSPROT;Acc:Q92545] 0.0372023 0.196899 0.188941031 TMEM131
2862 CGI-142; HEPATOMA-DERIVED GROWTH FACTOR 2. [RefSeq;Acc:NM_016073] no value
2863 ORAI3
2864 "PARKINSON DISEASE (AUTOSOMAL RECESSIVE, JUVENILE) 2, PARKIN ISOFORM 1; PARKIN. [RefSeq;Acc:NM_004562]" PARK2
2865 PROBABLE ATP-DEPENDENT RNA HELICASE P54 (ONCOGENE RCK) (DEAD-BOX PROTEIN 6). [SWISSPROT;Acc:P26196] 0.801671 4.24298 0.188940556 DDX6
2866 HEPATOMA-DERIVED GROWTH FACTOR-RELATED PROTEIN 2. [RefSeq;Acc:NM_032631] 0.0312313 0.165297 0.188940513 no value
2867 0.03085 0.163279 0.188940403 ORAI2
2868 60S RIBOSOMAL PROTEIN L8. [SWISSPROT;Acc:P25120] 0.0744045 0.393799 0.188940297 RPL8
2869 PC4 AND SFRS1 INTERACTING PROTEIN 2; PC4 AND SFRS1 INTERACTING PROTEIN 1; TRANSCRIPTIONAL COACTIVATOR P52/P75. [RefSeq;Acc:NM_033222] 0.0308872 0.163476 0.188940273 PSIP1
2870 HEPATOMA-DERIVED GROWTH FACTOR (HDGF) (HIGH-MOBILITY GROUP PROTEIN 1- LIKE 2) (HMG-1L2). [SWISSPROT;Acc:P51858] 0.0313429 0.165888 0.188940128 HDGF
2871 PWWP DOMAIN CONTAINING 1; HDGF (HEPATOMA-DERIVED GROWTH FACTOR) LIKE. [RefSeq;Acc:NM_138574] 0.0294363 0.155797 0.188940095 HDGFL1
2872 0.0371369 0.196598 0.188897649 no value
2873 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE BETA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 2) (1-AGPAT 2) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-BETA) (LPAAT-BETA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 2). [SWISSPROT;Acc:O15120] 0.198456 1.05097 0.18883127 AGPAT2
2874 "ENOYL-COA HYDRATASE, MITOCHONDRIAL PRECURSOR (EC 4.2.1.17) (SHORT CHAIN ENOYL-COA HYDRATASE) (SCEH) (ENOYL-COA HYDRATASE 1). [SWISSPROT;Acc:P30084]" 0.121508 0.643957 0.188689617 ECHS1
2875 "CATENIN (CADHERIN-ASSOCIATED PROTEIN), ALPHA-LIKE 1; ALPHA-CATULIN. [RefSeq;Acc:NM_003798]" 0.0374428 0.198705 0.188434111 CTNNAL1
2876 "SOLUTE CARRIER FAMILY 4 (ANION EXCHANGER), MEMBER 1, ADAPTOR PROTEIN; KIDNEY ANION EXCHANGER ADAPTOR PROTEIN; KANADAPTIN; LUNG CANCER ONCOGENE 3. [RefSeq;Acc:NM_018158]" SLC4A1AP
2877 CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT 2 (CKS-2). [SWISSPROT;Acc:P33552] 0.428065 2.2717 0.188433772 CKS2
2878 RET FINGER PROTEIN 2 (LEUKEMIA ASSOCIATED PROTEIN 5) (B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA TUMOR SUPPRESSOR LEU5) (PUTATIVE TUMOR SUPPRESSOR RFP2) (TRIPARTITE MOTIF PROTEIN 13). [SWISSPROT;Acc:O60858] 0.101998 0.546053 0.186791392 no value
2879 MALEYLACETOACETATE ISOMERASE (EC 5.2.1.2) (MAAI) (GLUTATHIONE S- TRANSFERASE ZETA 1) (EC 2.5.1.18) (GSTZ1-1). [SWISSPROT;Acc:O43708] 0.605608 3.24265 0.186763295 GSTZ1
2880 0.0513128 0.278146 0.184481531 CXorf56
2881 ADAPTER-RELATED PROTEIN COMPLEX 3 BETA 2 SUBUNIT (BETA-ADAPTIN 3B) (AP-3 COMPLEX BETA-3B SUBUNIT) (BETA-3B-ADAPTIN) (NEURON-SPECIFIC VESICLE COAT PROTEIN BETA-NAP). [SWISSPROT;Acc:Q13367] no value
2882 ADAPTER-RELATED PROTEIN COMPLEX 3 BETA 1 SUBUNIT (BETA-ADAPTIN 3A) (AP-3 COMPLEX BETA-3A SUBUNIT) (BETA-3A-ADAPTIN). [SWISSPROT;Acc:O00203] 0.0416917 0.225994 0.184481446 AP3B1
2883 NY-REN-24 ANTIGEN (FRAGMENT). [SPTREMBL;Acc:Q9Y5A4] 0.383948 2.08123 0.184481292 C19orf29
2884 "DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE, MITOCHONDRIAL PRECURSOR (EC 3.6.1.23) (DUTPASE) (DUTP PYROPHOSPHATASE). [SWISSPROT;Acc:P33316]" 0.158579 0.860412 0.184305891 DUT
2885 PROTEIN KINASE NYD-SP25. [RefSeq;Acc:NM_033516] 0.0532406 0.290193 0.183466176 TPD52L3
2886 MUSCLE-SPECIFIC BETA 1 INTEGRIN BINDING PROTEIN. [RefSeq;Acc:NM_014446] 0.0771117 0.428402 0.179998459 ITGB1BP3
2887 DIPEPTIDYLPEPTIDASE 9; DIPEPTIDYL PEPTIDASE 9; DIPEPTIDYL PEPTIDASE IV-RELATED PROTEIN-2. [RefSeq;Acc:NM_139159] 0.0368025 0.204515 0.179950126 DPP9
2888 DIPEPTIDYL PEPTIDASE 8 ISOFORM 2; DIPEPTIDYL PEPTIDASE 8. [RefSeq;Acc:NM_017743] 0.0310206 0.172385 0.179949532 DPP8
2889 0.0926874 0.515188 0.179909858 C9orf95
2890 0.050962 0.285736 0.178353445 SPTY2D1
2891 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 (EC 2.7.1.37) (HPDK1). [SWISSPROT;Acc:O15530] 0.61809 3.46554 0.178353157 PDPK1
2892 UBIQUITIN ACTIVATING ENZYME E1-LIKE PROTEIN. [RefSeq;Acc:NM_006395] 0.151451 0.850269 0.178121277 no value
2893 0.144225 0.822334 0.175384941 LASS5
2894 "PYRUVATE KINASE, M1 ISOZYME (EC 2.7.1.40) (PYRUVATE KINASE MUSCLE ISOZYME) (CYTOSOLIC THYROID HORMONE-BINDING PROTEIN) (CTHBP) (THBP1). [SWISSPROT;Acc:P14618]" 0.184777 1.05445 0.175235431 PKM2
2895 CELL DIVISION CONTROL PROTEIN 2 HOMOLOG (EC 2.7.1.-) (P34 PROTEIN KINASE) (CYCLIN-DEPENDENT KINASE 1) (CDK1). [SWISSPROT;Acc:P06493] 0.127708 0.729117 0.175154331 CDC2
2896 G2/MITOTIC-SPECIFIC CYCLIN B1. [SWISSPROT;Acc:P14635] 0.163112 0.9315 0.175106817 CCNB1
2897 CELL DIVISION PROTEIN KINASE 2 (EC 2.7.1.-) (P33 PROTEIN KINASE). [SWISSPROT;Acc:P24941] 0.141717 0.809352 0.175099339 CDK2
2898 G2/MITOTIC-SPECIFIC CYCLIN B2. [SWISSPROT;Acc:O95067] 0.201803 1.15298 0.175027321 CCNB2
2899 CELL DIVISION PROTEIN KINASE 3 (EC 2.7.1.-). [SWISSPROT;Acc:Q00526] 0.17249 0.985597 0.175010679 CDK3
2900 TRANSCRIPTION REPRESSOR P66 BETA COMPONENT OF THE MECP1 COMPLEX. [RefSeq;Acc:NM_020699] 0.0295551 0.169175 0.174701345 GATAD2B

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/