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 Hugo final
Results: HTML CSV LaTeX Showing element 2558 to 2607 of 3206 in total
Rank
description
measured
expected
Hugo
final
2558 ELONGATION FACTOR 2 (EF-2). [SWISSPROT;Acc:P13639] 0.432107 2.01624 EEF2 0.214313276
2559 0.128297 0.598643 CEP164 0.214313038
2560 AMYLOID BETA A4 PRECURSOR PROTEIN-BINDING FAMILY A MEMBER 1 (NEURON- SPECIFIC X11 PROTEIN) (NEURONAL MUNC18-1-INTERACTING PROTEIN 1) (MINT-1) (ADAPTER PROTEIN X11ALPHA). [SWISSPROT;Acc:Q02410] 0.16418 0.766097 APBA1 0.214307066
2561 "28S RIBOSOMAL PROTEIN S18A, MITOCHONDRIAL PRECURSOR (MRP-S18-A) (MRPS18A) (MRP-S18-3). [SWISSPROT;Acc:Q9NVS2]" 0.0319993 0.149576 MRPS18A 0.213933385
2562 "ATP SYNTHASE ALPHA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P25705]" 0.383439 1.79234 ATP5A1 0.213932066
2563 14-3-3 PROTEIN BETA/ALPHA (PROTEIN KINASE C INHIBITOR PROTEIN-1) (KCIP-1) (PROTEIN 1054). [SWISSPROT;Acc:P31946] 0.286436 1.34026 YWHAB 0.213716742
2564 GLUTAMINE SYNTHETASE (EC 6.3.1.2) (GLUTAMATE--AMMONIA LIGASE). [SWISSPROT;Acc:P15104] 0.174535 0.8167 GLUL 0.213707604
2565 TETRATRICOPEPTIDE REPEAT PROTEIN 4 (MY044 PROTEIN). [SWISSPROT;Acc:O95801] 0.061947 0.290115 no value 0.213525671
2566 3-HYDROXYISOBUTYRYL-COENZYME A HYDROLASE. [RefSeq;Acc:NM_014362] 0.512064 2.39827 0.213513908
2567 0.0789696 0.370007 ZYG11B 0.213427314
2568 HISTONE DEACETYLASE 5 (HD5) (ANTIGEN NY-CO-9). [SWISSPROT;Acc:Q9UQL6] 0.078494 0.367782 HDAC5 0.213425344
2569 HISTONE DEACETYLASE 4 (HD4). [SWISSPROT;Acc:P56524] 0.0642768 0.301176 HDAC4 0.213419396
2570 HISTONE DEACETYLASE 9 (HD9) (HD7B) (HD7). [SWISSPROT;Acc:Q9UKV0] 0.06311 0.29571 HDAC9 0.213418552
2571 SODIUM-DEPENDENT MULTIVITAMIN TRANSPORTER (NA(+)-DEPENDENT MULTIVITAMIN TRANSPORTER). [SWISSPROT;Acc:Q9Y289] 0.248255 1.16362 SLC5A6 0.213347141
2572 "SOLUTE CARRIER FAMILY 5 (IODIDE TRANSPORTER), MEMBER 8; APICAL IODIDE TRANSPORTER. [RefSeq;Acc:NM_145913]" 0.257307 1.20606 SLC5A8 0.213345107
2573 KIDNEY AND LIVER PROLINE OXIDASE 1. [RefSeq;Acc:NM_021232] 0.0574606 0.269336 PRODH2 0.2133417
2574 0.0577101 0.270506 no value 0.213341294
2575 SODIUM/IODIDE COTRANSPORTER (NA(+)/I(-) COTRANSPORTER) (SODIUM-IODIDE SYMPORTER) (NA+/I-SYMPORTER). [SWISSPROT;Acc:Q92911] 0.30514 1.43033 SLC5A5 0.213335384
2576 14-3-3 PROTEIN ZETA/DELTA (PROTEIN KINASE C INHIBITOR PROTEIN-1) (KCIP-1) (FACTOR ACTIVATING EXOENZYME S) (FAS). [SWISSPROT;Acc:P29312] 0.354694 1.66376 YWHAZ 0.2131882
2577 "SERINE PROTEASE HTRA2, MITOCHONDRIAL PRECURSOR (EC 3.4.21.-) (HIGH TEMPERATURE REQUIREMENT PROTEIN A2) (HTRA2) (OMI STRESS-REGULATED ENDOPROTEASE) (SERINE PROTEINASE OMI). [SWISSPROT;Acc:O43464]" 0.4666 2.18902 HTRA2 0.213154745
2578 PROBABLE SERINE PROTEASE HTRA4 PRECURSOR (EC 3.4.21.-). [SWISSPROT;Acc:P83105] 0.491713 2.30709 HTRA4 0.213131261
2579 PROBABLE SERINE PROTEASE HTRA3 PRECURSOR (EC 3.4.21.-). [SWISSPROT;Acc:P83110] 0.498067 2.33696 HTRA3 0.213126027
2580 BLOOD GROUP RH(CE) POLYPEPTIDE (RHESUS C/E ANTIGENS) (RH30A) (RHIXB) (RH POLYPEPTIDE 1) (RHPI). [SWISSPROT;Acc:P18577] 0.0564693 0.264963 no value 0.213121455
2581 BLOOD GROUP RH(D) POLYPEPTIDE (RHESUS D ANTIGEN) (RHXIII) (RH POLYPEPTIDE 2) (RHPII). [SWISSPROT;Acc:Q02161] RHD
2582 BLOOD GROUP RH(CE) POLYPEPTIDE (RHESUS C/E ANTIGENS) (RH30A) (RHIXB) (RH POLYPEPTIDE 1) (RHPI). [SWISSPROT;Acc:P18577] 0.0561617 0.26352 no value 0.213121205
2583 RHESUS BLOOD GROUP-ASSOCIATED GLYCOPROTEIN (ERYTHROCYTE PLASMA MEMBRANE 50 KDA GLYCOPROTEIN) (RH50A). [SWISSPROT;Acc:Q02094] 0.062927 0.295267 RHAG 0.213118974
2584 "RHESUS BLOOD GROUP, B GLYCOPROTEIN; RH TYPE B GLYCOPROTEIN. [RefSeq;Acc:NM_020407]" 0.0646696 0.303444 RHBG 0.21311873
2585 RH TYPE C GLYCOPROTEIN. [RefSeq;Acc:NM_016321] 0.077662 0.364414 RHCG 0.213114754
2586 SERINE PROTEASE HTRA1 PRECURSOR (EC 3.4.21.-) (L56). [SWISSPROT;Acc:Q92743] 0.574918 2.69828 HTRA1 0.213068325
2587 MYOFIBRILLOGENESIS REGULATOR 1; TRANS-ACTIVATED BY HEPATITIS C VIRUS CORE PROTEIN 2; LIKELY ORTHOLOG OF MOUSE BRAIN PROTEIN 17. [RefSeq;Acc:NM_022572] 0.48801 2.292 PNKD 0.212918848
2588 0.526405 2.47257 HAGHL 0.212897916
2589 "CALCIUM-BINDING MITOCHONDRIAL CARRIER PROTEIN ARALAR2 (SOLUTE CARRIER FAMILY 25, MEMBER 13) (CITRIN). [SWISSPROT;Acc:Q9UJS0]" 0.0223249 0.104865 SLC25A13 0.212891813
2590 DC11 PROTEIN. [RefSeq;Acc:NM_020186] 0.0255653 0.120086 no value 0.212891594
2591 MELANOMA ANTIGEN RECOGNIZED BY T CELLS 2. [RefSeq;Acc:NM_018194] HHAT
2592 HEPATITIS C VIRUS CORE-BINDING PROTEIN 6; CERVICAL CANCER ONCOGENE 3. [RefSeq;Acc:NM_023934] no value
2593 "CALCIUM-BINDING MITOCHONDRIAL CARRIER PROTEIN ARALAR1 (SOLUTE CARRIER FAMILY 25, MEMBER 12). [SWISSPROT;Acc:O75746]" 0.0255652 SLC25A12 0.212890762
2594 "UBIQUITIN-ACTIVATING ENZYME E1C (UBA3 HOMOLOG, YEAST); UBIQUITIN-ACTIVATING ENZYME E1C (HOMOLOGOUS TO YEAST UBA3). [RefSeq;Acc:NM_003968]" 0.0734554 0.345038 UBE1C 0.212890754
2595 "ACYL CARRIER PROTEIN, MITOCHONDRIAL PRECURSOR (ACP) (NADH-UBIQUINONE OXIDOREDUCTASE 9.6 KDA SUBUNIT) (CI-SDAP). [SWISSPROT;Acc:O14561]" 0.929425 4.36574 NDUFAB1 0.212890598
2596 "5-AMINOLEVULINIC ACID SYNTHASE, NONSPECIFIC, MITOCHONDRIAL PRECURSOR (EC 2.3.1.37) (DELTA-AMINOLEVULINATE SYNTHASE) (DELTA-ALA SYNTHETASE) (ALAS-H). [SWISSPROT;Acc:P13196]" 0.0634018 0.297814 ALAS1 0.212890596
2597 AMYLOID BETA PRECURSOR PROTEIN-BINDING PROTEIN 1; AMYLOID PROTEIN-BINDING PROTEIN 1. [RefSeq;Acc:NM_003905] 0.0719023 0.337743 APPBP1 0.212890571
2598 0.0200176 0.0940277 HHATL 0.212890457
2599 "5-AMINOLEVULINIC ACID SYNTHASE, ERYTHROID-SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 2.3.1.37) (DELTA-AMINOLEVULINATE SYNTHASE) (DELTA-ALA SYNTHETASE) (ALAS-E). [SWISSPROT;Acc:P22557]" 0.0766446 0.360019 ALAS2 0.212890431
2600 UBIQUITIN-ACTIVATING ENZYME E1 (A1S9 PROTEIN). [SWISSPROT;Acc:P22314] 0.046337 0.217657 UBE1 0.212890006
2601 YL-1 PROTEIN (TRANSCRIPTION FACTOR-LIKE 1). [SWISSPROT;Acc:Q15906] 0.0253936 0.119307 VPS72 0.212842499
2602 HYDROXYACYLGLUTATHIONE HYDROLASE (EC 3.1.2.6) (GLYOXALASE II) (GLX II). [SWISSPROT;Acc:Q16775] 0.687702 3.23104 HAGH 0.212842305
2603 DYSKERIN (NUCLEOLAR PROTEIN NAP57) (CBF5 HOMOLOG). [SWISSPROT;Acc:O60832] 0.95535 4.50581 DKC1 0.212026251
2604 "ACETYL-COA ACETYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.3.1.9) (ACETOACETYL-COA THIOLASE) (T2). [SWISSPROT;Acc:P24752]" 0.663698 3.13139 ACAT1 0.211949965
2605 "HYDROXYMETHYLGLUTARYL-COA SYNTHASE, MITOCHONDRIAL PRECURSOR (EC 2.3.3.10) (HMG-COA SYNTHASE) (3-HYDROXY-3-METHYLGLUTARYL COENZYME A SYNTHASE). [SWISSPROT;Acc:P54868]" 0.0635814 0.299985 HMGCS2 0.211948597
2606 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE (EC 1.1.1.34) (HMG-COA REDUCTASE). [SWISSPROT;Acc:P04035] 0.0963713 0.454692 HMGCR 0.211948528
2607 "HYDROXYMETHYLGLUTARYL-COA SYNTHASE, CYTOPLASMIC (EC 2.3.3.10) (HMG-COA SYNTHASE) (3-HYDROXY-3-METHYLGLUTARYL COENZYME A SYNTHASE). [SWISSPROT;Acc:Q01581]" 0.0751775 0.354697 HMGCS1 0.211948508

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/