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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final Rank Gene description measured expected Hugo
Results: HTML CSV LaTeX Showing element 501 to 550 of 3206 in total
final
Rank
description
measured
expected
Hugo
0.207413261 2706 "STEROID HORMONE RECEPTOR ERR2 (ESTROGEN-RELATED RECEPTOR, BETA) (ERR-BETA) (ESTROGEN RECEPTOR-LIKE 2) (ERR BETA-2). [SWISSPROT;Acc:O95718]" 0.175846 0.847805 ESRRB
0.207501483 2705 0.119287 0.574873 ABHD14B
0.207511104 2704 "CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 73 KDA SUBUNIT (CPSF 73 KDA SUBUNIT). [SWISSPROT;Acc:Q9UKF6]" 0.412088 1.98586 CPSF3
0.207643979 2703 MONOGLYCERIDE LIPASE; LYSOPHOSPHOLIPASE-LIKE. [RefSeq;Acc:NM_007283] 0.0986882 0.475276 MGLL
0.207676821 2702 0.145039 0.698388 FAM82B
0.20769734 2701 METAXIN 1. [SWISSPROT;Acc:Q13505] 0.133976 0.645054 MTX1
0.207766228 2700 0.0804074 0.387009 HNRPLL
0.207772065 2699 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN L (HNRNP L). [SWISSPROT;Acc:P14866] 0.100335 0.482909 HNRNPL
0.207810966 2698 ESTROGEN-RELATED RECEPTOR GAMMA (ESTROGEN RECEPTOR RELATED PROTEIN 3) (ERR GAMMA-2). [SWISSPROT;Acc:O75454] 0.151787 0.730409 no value
0.207985545 2697 "PROGRAMMED CELL DEATH PROTEIN 8, MITOCHONDRIAL PRECURSOR (EC 1.-.-.-) (APOPTOSIS-INDUCING FACTOR). [SWISSPROT;Acc:O95831]" 0.112229 0.5396 AIFM1
0.207986009 2696 "ENDONUCLEASE G, MITOCHONDRIAL PRECURSOR (EC 3.1.30.-) (ENDO G). [SWISSPROT;Acc:Q14249]" 0.0410294 0.19727 ENDOG
0.207986089 2695 T-BOX TRANSCRIPTION FACTOR TBX6 (T-BOX PROTEIN 6). [SWISSPROT;Acc:O95947] 0.018755 0.0901743 TBX6
0.208171009 2694 "STEROID HORMONE RECEPTOR ERR1 (ESTROGEN-RELATED RECEPTOR, ALPHA) (ERR-ALPHA) (ESTROGEN RECEPTOR-LIKE 1). [SWISSPROT;Acc:P11474]" 0.13519 0.649418 ESRRA
0.208211209 2693 0.122185 0.586832 AIFM3
0.20822235 2692 RETICULON 4 (NEURITE OUTGROWTH INHIBITOR) (NOGO PROTEIN) (FOOCEN) (NEUROENDOCRINE-SPECIFIC PROTEIN) (NSP) (NEUROENDOCRINE SPECIFIC PROTEIN C HOMOLOG) (RTN-X) (RETICULON 5) (MY043 PROTEIN). [SWISSPROT;Acc:Q9NQC3] 0.267978 1.28698 RTN4
0.20826922 2691 RETICULON 1 (NEUROENDOCRINE-SPECIFIC PROTEIN). [SWISSPROT;Acc:Q16799] 0.268811 1.29069 RTN1
0.208273539 2690 SIN3 ASSOCIATED POLYPEPTIDE P18 (2HOR0202). [SWISSPROT;Acc:O00422] 0.0937258 0.450013 SAP18
0.208283692 2689 EH-DOMAIN CONTAINING PROTEIN 2. [SWISSPROT;Acc:Q9NZN4] 0.0892656 0.428577 EHD2
0.208283782 2688 EH-DOMAIN CONTAINING PROTEIN 4 (EH DOMAIN-CONTAINING PROTEIN FKSG7) (HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN 10/11). [SWISSPROT;Acc:Q9H223] 0.0943663 0.453066 EHD4
0.208285345 2687 EH-DOMAIN CONTAINING PROTEIN 3. [SWISSPROT;Acc:Q9NZN3] 0.107786 0.517492 EHD3
0.208285996 2686 EH-DOMAIN CONTAINING PROTEIN 1 (TESTILIN) (HPAST1). [SWISSPROT;Acc:Q9H4M9] 0.121 0.580932 EHD1
0.208330664 2685 RETICULON PROTEIN 2 (NEUROENDOCRINE-SPECIFIC PROTEIN-LIKE 1) (NSP-LIKE PROTEIN 1) (NSPLI). [SWISSPROT;Acc:O75298] 0.175589 0.842838 RTN2
0.20833468 2684 POLY(A) POLYMERASE ALPHA (EC 2.7.7.19) (PAP) (POLYNUCLEOTIDE ADENYLYLTRANSFERASE ALPHA) (FRAGMENT). [SWISSPROT;Acc:P51003] 0.438432 2.10446 PAPOLA
0.208345578 2683 RETICULON PROTEIN 3 (NEUROENDOCRINE-SPECIFIC PROTEIN-LIKE 2) (NSP-LIKE PROTEIN II) (NSPLII). [SWISSPROT;Acc:O95197] 0.203468 0.976589 RTN3
0.208386587 2682 EXOCYST COMPLEX COMPONENT SEC5. [SWISSPROT;Acc:Q96KP1] 0.0545554 0.261799 EXOC2
0.208417823 2681 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7 INTERACTING PROTEIN 1 (TAK1-BINDING PROTEIN 1). [SWISSPROT;Acc:Q15750] 0.225506 1.08199 MAP3K7IP1
0.20844841 2680 POLY(A) POLYMERASE GAMMA (EC 2.7.7.19) (PAP GAMMA) (POLYNUCLEOTIDE ADENYLYLTRANSFERASE GAMMA) (SRP RNA 3' ADENYLATING ENZYME). [SWISSPROT;Acc:Q9BWT3] 0.377523 1.81111 PAPOLG
0.208587354 2679 "ACYL-COENZYME A OXIDASE 2, PEROXISOMAL (EC 1.3.3.6) (BRANCHED-CHAIN ACYL-COA OXIDASE) (BRCACOX) (TRIHYDROXYCOPROSTANOYL-COA OXIDASE) (THCCOX) (THCA-COA OXIDASE). [SWISSPROT;Acc:Q99424]" 0.663483 3.18084 ACOX2
0.208724659 2678 UDP-GLUCOSE 4-EPIMERASE (EC 5.1.3.2) (GALACTOWALDENASE) (UDP- GALACTOSE 4-EPIMERASE). [SWISSPROT;Acc:Q14376] 0.234953 1.12566 GALE
0.208724931 2677 GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE (EC 2.7.7.12) (GAL-1-P URIDYLYLTRANSFERASE) (UDP-GLUCOSE--HEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE). [SWISSPROT;Acc:P07902] 0.0454701 0.217847 no value
0.208725208 2676 N-ACETYLGALACTOSAMINE KINASE (EC 2.7.1.-) (GALNAC KINASE) (GALACTOKINASE 2). [SWISSPROT;Acc:Q01415] 0.0435693 0.20874 GALK2
0.208743979 2675 "TBP-ASSOCIATED FACTOR 9L; NEURONAL CELL DEATH-RELATED PROTEIN; TAF9-LIKE RNA POLYMERASE II, TATA BOX BINDING PROTEIN (TBP)-ASSOCIATED FACTOR, 31 KD; NEURONAL CELL DEATH-RELATED GENE IN NEURON-7; TRANSCRIPTION ASSOCIATED FACTOR TAFII31L; TRANSCRIPTION INIT" 0.383112 1.83532 TAF9B
0.209232319 2674 CELL ADHESION MOLECULE WITH HOMOLOGY TO L1CAM PRECURSOR; NEURAL CELL ADHESION MOLECULE; CELL ADHESION MOLECULE L1-LIKE; L1 CELL ADHESION MOLECULE 2. [RefSeq;Acc:NM_006614] 0.0249248 0.119125 CHL1
0.209232704 2673 0.0251255 0.120084 NFASC
0.209232998 2672 TRANSCRIPTION FACTOR MAFK (ERYTHROID TRANSCRIPTION FACTOR NF-E2 P18 SUBUNIT). [SWISSPROT;Acc:O60675] 0.0897053 0.428734 no value
0.209233039 2671 "NUCLEAR FACTOR ERYTHROID 2 RELATED FACTOR 1 (NF-E2 RELATED FACTOR 1) (NFE2-RELATED FACTOR 1) (NUCLEAR FACTOR, ERYTHROID DERIVED 2, LIKE 1) (TRANSCRIPTION FACTOR 11) (TRANSCRIPTION FACTOR HBZ17) (TRANSCRIPTION FACTOR LCR-F1) (LOCUS CONTROL REGION-FACTOR 1)" 0.0693641 0.331516 NFE2L1
0.209233273 2670 TRANSCRIPTION FACTOR MAFG (V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG G) (HMAF). [SWISSPROT;Acc:O15525] 0.0798317 0.381544 no value
0.209233327 2669 TRANSCRIPTION INITIATION FACTOR TFIID 31 KDA SUBUNIT (TAFII-31) (TAFII-32) (TAFII32). [SWISSPROT;Acc:Q16594] 0.61918 2.95928 TAF9
0.209233395 2668 NUCLEAR FACTOR (ERYTHROID-DERIVED 2)-LIKE 3; NF-E2-RELATED FACTOR 3. [RefSeq;Acc:NM_004289] 0.0877868 0.419564 NFE2L3
0.209233438 2667 TRANSCRIPTION FACTOR MAFF (V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG F) (U-MAF). [SWISSPROT;Acc:Q9ULX9] 0.0761231 0.363819 MAFF
0.209233775 2666 NEURAL CELL ADHESION MOLECULE L1 PRECURSOR (N-CAM L1) (CD171 ANTIGEN). [SWISSPROT;Acc:P32004] 0.02527 0.120774 no value
0.209244667 2665 ASPARTYL-TRNA SYNTHETASE (EC 6.1.1.12) (ASPARTATE--TRNA LIGASE) (ASPRS). [SWISSPROT;Acc:P14868] 0.149127 0.712692 DARS
0.209349737 2664 DEOXYCYTIDYLATE DEAMINASE (EC 3.5.4.12) (DCMP DEAMINASE). [SWISSPROT;Acc:P32321] 0.124149 0.593022 DCTD
0.209431 2663 POLYMYOSITIS/SCLERODERMA AUTOANTIGEN 2 (AUTOANTIGEN PM/SCL 2) (POLYMYOSITIS/SCLERODERMA AUTOANTIGEN 100 KDA) (PM/SCL-100) (P100 POLYMYOSITIS-SCLERODERMA OVERLAP SYNDROME ASSOCIATED AUTOANTIGEN). [SWISSPROT;Acc:Q01780] 0.474956 2.26784 EXOSC10
0.209588524 2662 "ELECTRON TRANSFER FLAVOPROTEIN-UBIQUINONE OXIDOREDUCTASE, MITOCHONDRIAL PRECURSOR (EC 1.5.5.1) (ETF-QO) (ETF-UBIQUINONE OXIDOREDUCTASE) (ETF DEHYDROGENASE) (ELECTRON-TRANSFERRING- FLAVOPROTEIN DEHYDROGENASE). [SWISSPROT;Acc:Q16134]" 0.114957 0.548489 ETFDH
0.209906836 2661 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 0.558539 2.66089 CDS1
0.209937671 2660 "SOLUTE CARRIER FAMILY 13, MEMBER 2 (RENAL SODIUM/DICARBOXYLATE COTRANSPORTER) (NA(+)/DICARBOXYLATE COTRANSPORTER 1) (NADC-1). [SWISSPROT;Acc:Q13183]" 0.0401827 0.191403 SLC13A2
0.209937848 2659 "SOLUTE CARRIER FAMILY 13, MEMBER 1 (RENAL SODIUM/SULFATE COTRANSPORTER) (NA(+)/SULFATE COTRANSPORTER) (HNASI-1). [SWISSPROT;Acc:Q9BZW2]" 0.0481673 0.229436 SLC13A1
0.209937875 2658 "SOLUTE CARRIER FAMILY 13, MEMBER 4 (NA+/SULFATE COTRANSPORTER SUT-1). [SWISSPROT;Acc:Q9UKG4]" 0.0480531 0.228892 SLC13A4
0.209937924 2657 "SOLUTE CARRIER FAMILY 13, MEMBER 3 (SODIUM-DEPENDENT HIGH-AFFINITY DICARBOXYLATE TRANSPORTER 2) (NA(+)/DICARBOXYLATE COTRANSPORTER 3) (NADC-3) (HNADC3). [SWISSPROT;Acc:Q8WWT9]" 0.0395353 0.188319 SLC13A3

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/