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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
final expected Gene measured Rank description Hugo
Results: HTML CSV LaTeX Showing element 502 to 551 of 3206 in total
final
expected
measured
Rank
description
Hugo
0.207501483 0.574873 0.119287 2705 ABHD14B
0.207511104 1.98586 0.412088 2704 "CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 73 KDA SUBUNIT (CPSF 73 KDA SUBUNIT). [SWISSPROT;Acc:Q9UKF6]" CPSF3
0.207643979 0.475276 0.0986882 2703 MONOGLYCERIDE LIPASE; LYSOPHOSPHOLIPASE-LIKE. [RefSeq;Acc:NM_007283] MGLL
0.207676821 0.698388 0.145039 2702 FAM82B
0.20769734 0.645054 0.133976 2701 METAXIN 1. [SWISSPROT;Acc:Q13505] MTX1
0.207766228 0.387009 0.0804074 2700 HNRPLL
0.207772065 0.482909 0.100335 2699 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN L (HNRNP L). [SWISSPROT;Acc:P14866] HNRNPL
0.207810966 0.730409 0.151787 2698 ESTROGEN-RELATED RECEPTOR GAMMA (ESTROGEN RECEPTOR RELATED PROTEIN 3) (ERR GAMMA-2). [SWISSPROT;Acc:O75454] no value
0.207985545 0.5396 0.112229 2697 "PROGRAMMED CELL DEATH PROTEIN 8, MITOCHONDRIAL PRECURSOR (EC 1.-.-.-) (APOPTOSIS-INDUCING FACTOR). [SWISSPROT;Acc:O95831]" AIFM1
0.207986009 0.19727 0.0410294 2696 "ENDONUCLEASE G, MITOCHONDRIAL PRECURSOR (EC 3.1.30.-) (ENDO G). [SWISSPROT;Acc:Q14249]" ENDOG
0.207986089 0.0901743 0.018755 2695 T-BOX TRANSCRIPTION FACTOR TBX6 (T-BOX PROTEIN 6). [SWISSPROT;Acc:O95947] TBX6
0.208171009 0.649418 0.13519 2694 "STEROID HORMONE RECEPTOR ERR1 (ESTROGEN-RELATED RECEPTOR, ALPHA) (ERR-ALPHA) (ESTROGEN RECEPTOR-LIKE 1). [SWISSPROT;Acc:P11474]" ESRRA
0.208211209 0.586832 0.122185 2693 AIFM3
0.20822235 1.28698 0.267978 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] RTN4
0.20826922 1.29069 0.268811 2691 RETICULON 1 (NEUROENDOCRINE-SPECIFIC PROTEIN). [SWISSPROT;Acc:Q16799] RTN1
0.208273539 0.450013 0.0937258 2690 SIN3 ASSOCIATED POLYPEPTIDE P18 (2HOR0202). [SWISSPROT;Acc:O00422] SAP18
0.208283692 0.428577 0.0892656 2689 EH-DOMAIN CONTAINING PROTEIN 2. [SWISSPROT;Acc:Q9NZN4] EHD2
0.208283782 0.453066 0.0943663 2688 EH-DOMAIN CONTAINING PROTEIN 4 (EH DOMAIN-CONTAINING PROTEIN FKSG7) (HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN 10/11). [SWISSPROT;Acc:Q9H223] EHD4
0.208285345 0.517492 0.107786 2687 EH-DOMAIN CONTAINING PROTEIN 3. [SWISSPROT;Acc:Q9NZN3] EHD3
0.208285996 0.580932 0.121 2686 EH-DOMAIN CONTAINING PROTEIN 1 (TESTILIN) (HPAST1). [SWISSPROT;Acc:Q9H4M9] EHD1
0.208330664 0.842838 0.175589 2685 RETICULON PROTEIN 2 (NEUROENDOCRINE-SPECIFIC PROTEIN-LIKE 1) (NSP-LIKE PROTEIN 1) (NSPLI). [SWISSPROT;Acc:O75298] RTN2
0.20833468 2.10446 0.438432 2684 POLY(A) POLYMERASE ALPHA (EC 2.7.7.19) (PAP) (POLYNUCLEOTIDE ADENYLYLTRANSFERASE ALPHA) (FRAGMENT). [SWISSPROT;Acc:P51003] PAPOLA
0.208345578 0.976589 0.203468 2683 RETICULON PROTEIN 3 (NEUROENDOCRINE-SPECIFIC PROTEIN-LIKE 2) (NSP-LIKE PROTEIN II) (NSPLII). [SWISSPROT;Acc:O95197] RTN3
0.208386587 0.261799 0.0545554 2682 EXOCYST COMPLEX COMPONENT SEC5. [SWISSPROT;Acc:Q96KP1] EXOC2
0.208417823 1.08199 0.225506 2681 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7 INTERACTING PROTEIN 1 (TAK1-BINDING PROTEIN 1). [SWISSPROT;Acc:Q15750] MAP3K7IP1
0.20844841 1.81111 0.377523 2680 POLY(A) POLYMERASE GAMMA (EC 2.7.7.19) (PAP GAMMA) (POLYNUCLEOTIDE ADENYLYLTRANSFERASE GAMMA) (SRP RNA 3' ADENYLATING ENZYME). [SWISSPROT;Acc:Q9BWT3] PAPOLG
0.208587354 3.18084 0.663483 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]" ACOX2
0.208724659 1.12566 0.234953 2678 UDP-GLUCOSE 4-EPIMERASE (EC 5.1.3.2) (GALACTOWALDENASE) (UDP- GALACTOSE 4-EPIMERASE). [SWISSPROT;Acc:Q14376] GALE
0.208724931 0.217847 0.0454701 2677 GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE (EC 2.7.7.12) (GAL-1-P URIDYLYLTRANSFERASE) (UDP-GLUCOSE--HEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE). [SWISSPROT;Acc:P07902] no value
0.208725208 0.20874 0.0435693 2676 N-ACETYLGALACTOSAMINE KINASE (EC 2.7.1.-) (GALNAC KINASE) (GALACTOKINASE 2). [SWISSPROT;Acc:Q01415] GALK2
0.208743979 1.83532 0.383112 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" TAF9B
0.209232319 0.119125 0.0249248 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] CHL1
0.209232704 0.120084 0.0251255 2673 NFASC
0.209232998 0.428734 0.0897053 2672 TRANSCRIPTION FACTOR MAFK (ERYTHROID TRANSCRIPTION FACTOR NF-E2 P18 SUBUNIT). [SWISSPROT;Acc:O60675] no value
0.209233039 0.331516 0.0693641 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)" NFE2L1
0.209233273 0.381544 0.0798317 2670 TRANSCRIPTION FACTOR MAFG (V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG G) (HMAF). [SWISSPROT;Acc:O15525] no value
0.209233327 2.95928 0.61918 2669 TRANSCRIPTION INITIATION FACTOR TFIID 31 KDA SUBUNIT (TAFII-31) (TAFII-32) (TAFII32). [SWISSPROT;Acc:Q16594] TAF9
0.209233395 0.419564 0.0877868 2668 NUCLEAR FACTOR (ERYTHROID-DERIVED 2)-LIKE 3; NF-E2-RELATED FACTOR 3. [RefSeq;Acc:NM_004289] NFE2L3
0.209233438 0.363819 0.0761231 2667 TRANSCRIPTION FACTOR MAFF (V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG F) (U-MAF). [SWISSPROT;Acc:Q9ULX9] MAFF
0.209233775 0.120774 0.02527 2666 NEURAL CELL ADHESION MOLECULE L1 PRECURSOR (N-CAM L1) (CD171 ANTIGEN). [SWISSPROT;Acc:P32004] no value
0.209244667 0.712692 0.149127 2665 ASPARTYL-TRNA SYNTHETASE (EC 6.1.1.12) (ASPARTATE--TRNA LIGASE) (ASPRS). [SWISSPROT;Acc:P14868] DARS
0.209349737 0.593022 0.124149 2664 DEOXYCYTIDYLATE DEAMINASE (EC 3.5.4.12) (DCMP DEAMINASE). [SWISSPROT;Acc:P32321] DCTD
0.209431 2.26784 0.474956 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] EXOSC10
0.209588524 0.548489 0.114957 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]" ETFDH
0.209906836 2.66089 0.558539 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 CDS1
0.209937671 0.191403 0.0401827 2660 "SOLUTE CARRIER FAMILY 13, MEMBER 2 (RENAL SODIUM/DICARBOXYLATE COTRANSPORTER) (NA(+)/DICARBOXYLATE COTRANSPORTER 1) (NADC-1). [SWISSPROT;Acc:Q13183]" SLC13A2
0.209937848 0.229436 0.0481673 2659 "SOLUTE CARRIER FAMILY 13, MEMBER 1 (RENAL SODIUM/SULFATE COTRANSPORTER) (NA(+)/SULFATE COTRANSPORTER) (HNASI-1). [SWISSPROT;Acc:Q9BZW2]" SLC13A1
0.209937875 0.228892 0.0480531 2658 "SOLUTE CARRIER FAMILY 13, MEMBER 4 (NA+/SULFATE COTRANSPORTER SUT-1). [SWISSPROT;Acc:Q9UKG4]" SLC13A4
0.209937924 0.188319 0.0395353 2657 "SOLUTE CARRIER FAMILY 13, MEMBER 3 (SODIUM-DEPENDENT HIGH-AFFINITY DICARBOXYLATE TRANSPORTER 2) (NA(+)/DICARBOXYLATE COTRANSPORTER 3) (NADC-3) (HNADC3). [SWISSPROT;Acc:Q8WWT9]" SLC13A3
0.209942695 0.221972 0.0466014 2656 SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 1. [SWISSPROT;Acc:O15126] SCAMP1

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/