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 measured Gene expected description Hugo final
Results: HTML CSV LaTeX Showing element 2658 to 2707 of 3206 in total
Rank
measured
expected
description
Hugo
final
2658 0.0480531 0.228892 "SOLUTE CARRIER FAMILY 13, MEMBER 4 (NA+/SULFATE COTRANSPORTER SUT-1). [SWISSPROT;Acc:Q9UKG4]" SLC13A4 0.209937875
2659 0.0481673 0.229436 "SOLUTE CARRIER FAMILY 13, MEMBER 1 (RENAL SODIUM/SULFATE COTRANSPORTER) (NA(+)/SULFATE COTRANSPORTER) (HNASI-1). [SWISSPROT;Acc:Q9BZW2]" SLC13A1 0.209937848
2660 0.0401827 0.191403 "SOLUTE CARRIER FAMILY 13, MEMBER 2 (RENAL SODIUM/DICARBOXYLATE COTRANSPORTER) (NA(+)/DICARBOXYLATE COTRANSPORTER 1) (NADC-1). [SWISSPROT;Acc:Q13183]" SLC13A2 0.209937671
2661 0.558539 2.66089 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 CDS1 0.209906836
2662 0.114957 0.548489 "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]" ETFDH 0.209588524
2663 0.474956 2.26784 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] EXOSC10 0.209431
2664 0.124149 0.593022 DEOXYCYTIDYLATE DEAMINASE (EC 3.5.4.12) (DCMP DEAMINASE). [SWISSPROT;Acc:P32321] DCTD 0.209349737
2665 0.149127 0.712692 ASPARTYL-TRNA SYNTHETASE (EC 6.1.1.12) (ASPARTATE--TRNA LIGASE) (ASPRS). [SWISSPROT;Acc:P14868] DARS 0.209244667
2666 0.02527 0.120774 NEURAL CELL ADHESION MOLECULE L1 PRECURSOR (N-CAM L1) (CD171 ANTIGEN). [SWISSPROT;Acc:P32004] no value 0.209233775
2667 0.0761231 0.363819 TRANSCRIPTION FACTOR MAFF (V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG F) (U-MAF). [SWISSPROT;Acc:Q9ULX9] MAFF 0.209233438
2668 0.0877868 0.419564 NUCLEAR FACTOR (ERYTHROID-DERIVED 2)-LIKE 3; NF-E2-RELATED FACTOR 3. [RefSeq;Acc:NM_004289] NFE2L3 0.209233395
2669 0.61918 2.95928 TRANSCRIPTION INITIATION FACTOR TFIID 31 KDA SUBUNIT (TAFII-31) (TAFII-32) (TAFII32). [SWISSPROT;Acc:Q16594] TAF9 0.209233327
2670 0.0798317 0.381544 TRANSCRIPTION FACTOR MAFG (V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG G) (HMAF). [SWISSPROT;Acc:O15525] no value 0.209233273
2671 0.0693641 0.331516 "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)" NFE2L1 0.209233039
2672 0.0897053 0.428734 TRANSCRIPTION FACTOR MAFK (ERYTHROID TRANSCRIPTION FACTOR NF-E2 P18 SUBUNIT). [SWISSPROT;Acc:O60675] no value 0.209232998
2673 0.0251255 0.120084 NFASC 0.209232704
2674 0.0249248 0.119125 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] CHL1 0.209232319
2675 0.383112 1.83532 "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" TAF9B 0.208743979
2676 0.0435693 0.20874 N-ACETYLGALACTOSAMINE KINASE (EC 2.7.1.-) (GALNAC KINASE) (GALACTOKINASE 2). [SWISSPROT;Acc:Q01415] GALK2 0.208725208
2677 0.0454701 0.217847 GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE (EC 2.7.7.12) (GAL-1-P URIDYLYLTRANSFERASE) (UDP-GLUCOSE--HEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE). [SWISSPROT;Acc:P07902] no value 0.208724931
2678 0.234953 1.12566 UDP-GLUCOSE 4-EPIMERASE (EC 5.1.3.2) (GALACTOWALDENASE) (UDP- GALACTOSE 4-EPIMERASE). [SWISSPROT;Acc:Q14376] GALE 0.208724659
2679 0.663483 3.18084 "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]" ACOX2 0.208587354
2680 0.377523 1.81111 POLY(A) POLYMERASE GAMMA (EC 2.7.7.19) (PAP GAMMA) (POLYNUCLEOTIDE ADENYLYLTRANSFERASE GAMMA) (SRP RNA 3' ADENYLATING ENZYME). [SWISSPROT;Acc:Q9BWT3] PAPOLG 0.20844841
2681 0.225506 1.08199 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7 INTERACTING PROTEIN 1 (TAK1-BINDING PROTEIN 1). [SWISSPROT;Acc:Q15750] MAP3K7IP1 0.208417823
2682 0.0545554 0.261799 EXOCYST COMPLEX COMPONENT SEC5. [SWISSPROT;Acc:Q96KP1] EXOC2 0.208386587
2683 0.203468 0.976589 RETICULON PROTEIN 3 (NEUROENDOCRINE-SPECIFIC PROTEIN-LIKE 2) (NSP-LIKE PROTEIN II) (NSPLII). [SWISSPROT;Acc:O95197] RTN3 0.208345578
2684 0.438432 2.10446 POLY(A) POLYMERASE ALPHA (EC 2.7.7.19) (PAP) (POLYNUCLEOTIDE ADENYLYLTRANSFERASE ALPHA) (FRAGMENT). [SWISSPROT;Acc:P51003] PAPOLA 0.20833468
2685 0.175589 0.842838 RETICULON PROTEIN 2 (NEUROENDOCRINE-SPECIFIC PROTEIN-LIKE 1) (NSP-LIKE PROTEIN 1) (NSPLI). [SWISSPROT;Acc:O75298] RTN2 0.208330664
2686 0.121 0.580932 EH-DOMAIN CONTAINING PROTEIN 1 (TESTILIN) (HPAST1). [SWISSPROT;Acc:Q9H4M9] EHD1 0.208285996
2687 0.107786 0.517492 EH-DOMAIN CONTAINING PROTEIN 3. [SWISSPROT;Acc:Q9NZN3] EHD3 0.208285345
2688 0.0943663 0.453066 EH-DOMAIN CONTAINING PROTEIN 4 (EH DOMAIN-CONTAINING PROTEIN FKSG7) (HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN 10/11). [SWISSPROT;Acc:Q9H223] EHD4 0.208283782
2689 0.0892656 0.428577 EH-DOMAIN CONTAINING PROTEIN 2. [SWISSPROT;Acc:Q9NZN4] EHD2 0.208283692
2690 0.0937258 0.450013 SIN3 ASSOCIATED POLYPEPTIDE P18 (2HOR0202). [SWISSPROT;Acc:O00422] SAP18 0.208273539
2691 0.268811 1.29069 RETICULON 1 (NEUROENDOCRINE-SPECIFIC PROTEIN). [SWISSPROT;Acc:Q16799] RTN1 0.20826922
2692 0.267978 1.28698 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] RTN4 0.20822235
2693 0.122185 0.586832 AIFM3 0.208211209
2694 0.13519 0.649418 "STEROID HORMONE RECEPTOR ERR1 (ESTROGEN-RELATED RECEPTOR, ALPHA) (ERR-ALPHA) (ESTROGEN RECEPTOR-LIKE 1). [SWISSPROT;Acc:P11474]" ESRRA 0.208171009
2695 0.018755 0.0901743 T-BOX TRANSCRIPTION FACTOR TBX6 (T-BOX PROTEIN 6). [SWISSPROT;Acc:O95947] TBX6 0.207986089
2696 0.0410294 0.19727 "ENDONUCLEASE G, MITOCHONDRIAL PRECURSOR (EC 3.1.30.-) (ENDO G). [SWISSPROT;Acc:Q14249]" ENDOG 0.207986009
2697 0.112229 0.5396 "PROGRAMMED CELL DEATH PROTEIN 8, MITOCHONDRIAL PRECURSOR (EC 1.-.-.-) (APOPTOSIS-INDUCING FACTOR). [SWISSPROT;Acc:O95831]" AIFM1 0.207985545
2698 0.151787 0.730409 ESTROGEN-RELATED RECEPTOR GAMMA (ESTROGEN RECEPTOR RELATED PROTEIN 3) (ERR GAMMA-2). [SWISSPROT;Acc:O75454] no value 0.207810966
2699 0.100335 0.482909 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN L (HNRNP L). [SWISSPROT;Acc:P14866] HNRNPL 0.207772065
2700 0.0804074 0.387009 HNRPLL 0.207766228
2701 0.133976 0.645054 METAXIN 1. [SWISSPROT;Acc:Q13505] MTX1 0.20769734
2702 0.145039 0.698388 FAM82B 0.207676821
2703 0.0986882 0.475276 MONOGLYCERIDE LIPASE; LYSOPHOSPHOLIPASE-LIKE. [RefSeq;Acc:NM_007283] MGLL 0.207643979
2704 0.412088 1.98586 "CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 73 KDA SUBUNIT (CPSF 73 KDA SUBUNIT). [SWISSPROT;Acc:Q9UKF6]" CPSF3 0.207511104
2705 0.119287 0.574873 ABHD14B 0.207501483
2706 0.175846 0.847805 "STEROID HORMONE RECEPTOR ERR2 (ESTROGEN-RELATED RECEPTOR, BETA) (ERR-BETA) (ESTROGEN RECEPTOR-LIKE 2) (ERR BETA-2). [SWISSPROT;Acc:O95718]" ESRRB 0.207413261
2707 0.542979 2.61855 no value 0.207358653

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/