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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Hugo Rank Gene measured description expected final
Results: HTML CSV LaTeX Showing element 551 to 600 of 3206 in total
Hugo
Rank
measured
description
expected
final
ATP13A2 1189 0.0305968 PROBABLE CATION-TRANSPORTING ATPASE 1 (EC 3.6.1.-). [SWISSPROT;Acc:Q9NQ11] 0.123075 0.248602884
ATP13A4 1192 0.0386201 0.155349 0.24860218
ATP1A1 1032 0.063502 SODIUM/POTASSIUM-TRANSPORTING ATPASE ALPHA-1 CHAIN PRECURSOR (EC 3.6.3.9) (SODIUM PUMP 1) (NA+/K+ ATPASE 1). [SWISSPROT;Acc:P05023] 0.250657 0.253342217
ATP1A2 1031 SODIUM/POTASSIUM-TRANSPORTING ATPASE ALPHA-2 CHAIN PRECURSOR (EC 3.6.3.9) (SODIUM PUMP 2) (NA+/K+ ATPASE 2). [SWISSPROT;Acc:P50993]
ATP1A3 1034 0.0735677 SODIUM/POTASSIUM-TRANSPORTING ATPASE ALPHA-3 CHAIN (EC 3.6.3.9) (SODIUM PUMP 3) (NA+/K+ ATPASE 3) (ALPHA(III)). [SWISSPROT;Acc:P13637] 0.290389 0.253341897
ATP2C1 1455 0.0944765 "CALCIUM-TRANSPORTING ATPASE TYPE 2C, MEMBER 1 (EC 3.6.3.8) (ATPASE 2C1) (ATP-DEPENDENT CA(2+) PUMP PMR1) (HUSSY-28). [SWISSPROT;Acc:P98194]" 0.388558 0.243146454
ATP2C2 1450 0.0721789 PROBABLE CALCIUM-TRANSPORTING ATPASE KIAA0703 (EC 3.6.3.8). [SWISSPROT;Acc:O75185] 0.296552 0.243393739
ATP5A1 2562 0.383439 "ATP SYNTHASE ALPHA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P25705]" 1.79234 0.213932066
ATP5B 2262 0.366428 "ATP SYNTHASE BETA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P06576]" 1.64277 0.223054962
ATP5C1 2245 0.28274 "ATP SYNTHASE GAMMA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P36542]" 1.26423 0.223646014
ATP5D 2391 0.301597 "ATP SYNTHASE DELTA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P30049]" 1.37291 0.219677182
ATP5F1 212 0.155654 "ATP SYNTHASE B CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P24539]" 0.485577 0.320554721
ATP5J2 2612 0.0258274 "ATP SYNTHASE F CHAIN, MITOCHONDRIAL (EC 3.6.3.14). [SWISSPROT;Acc:P56134]" 0.122212 0.211332766
ATP5O 2246 0.28274 "ATP SYNTHASE OLIGOMYCIN SENSITIVITY CONFERRAL PROTEIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14) (OSCP). [SWISSPROT;Acc:P48047]" 1.26423 0.223646014
ATP5S 1795 0.0303657 "ATP SYNTHASE COUPLING FACTOR B, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:Q99766]" 0.129305 0.234837787
ATP6V0A1 1716 0.269961 VACUOLAR PROTON TRANSLOCATING ATPASE 116 KDA SUBUNIT A ISOFORM 1 (CLATHRIN-COATED VESICLE/SYNAPTIC VESICLE PROTON PUMP 116 KDA SUBUNIT) (VACUOLAR PROTON PUMP SUBUNIT 1) (VACUOLAR ADENOSINE TRIPHOSPHATASE SUBUNIT AC116). [SWISSPROT;Acc:Q93050] 1.13756 0.237315834
ATP6V0A2 1718 0.211834 VACUOLAR PROTON TRANSLOCATING ATPASE 116 KDA SUBUNIT A ISOFORM 2 (V-ATPASE 116-KDA ISOFORM A2) (TJ6). [SWISSPROT;Acc:Q9Y487] 0.892673 0.237303021
ATP6V0A4 1717 0.224133 "ATPASE, H+ TRANSPORTING, LYSOSOMAL V0 SUBUNIT A ISOFORM 4; VACUOLAR PROTON PUMP 116 KDA ACCESSORY SUBUNIT; VACUOLAR PROTON PUMP, SUBUNIT 2; H(+)-TRANSPORTING TWO-SECTOR ATPASE, NONCATALYTIC ACCESSORY PROTEIN 1B; ATPASE, H+ TRANSPORTING, LYSOSOMAL (VACUOLA" 0.944489 0.237306099
ATP6V0B 1879 0.465943 VACUOLAR ATP SYNTHASE 21 KDA PROTEOLIPID SUBUNIT (EC 3.6.3.14) (HATPL). [SWISSPROT;Acc:Q99437] 2.00171 0.23277248
ATP6V0C 1880 0.556589 VACUOLAR ATP SYNTHASE 16 KDA PROTEOLIPID SUBUNIT (EC 3.6.3.14). [SWISSPROT;Acc:P27449] 2.39113 0.232772371
ATP6V0D1 1548 0.584458 VACUOLAR ATP SYNTHASE SUBUNIT D (EC 3.6.3.14) (V-ATPASE D SUBUNIT) (VACUOLAR PROTON PUMP D SUBUNIT) (V-ATPASE AC39 SUBUNIT) (V-ATPASE 40 KDA ACCESSORY PROTEIN) (P39) (32 KDA ACCESSORY PROTEIN). [SWISSPROT;Acc:P12953] 2.4172 0.241791329
ATP6V0D2 1763 0.33278 "ATPASE, H+ TRANSPORTING, LYSOSOMAL 38KDA, V0 SUBUNIT D ISOFORM 2. [RefSeq;Acc:NM_152565]" 1.40872 0.236228633
ATP6V1A 1698 0.712561 "VACUOLAR ATP SYNTHASE CATALYTIC SUBUNIT A, UBIQUITOUS ISOFORM (EC 3.6.3.14) (V-ATPASE A SUBUNIT 1) (VACUOLAR PROTON PUMP ALPHA SUBUNIT 1) (V-ATPASE 69 KDA SUBUNIT 1) (ISOFORM VA68). [SWISSPROT;Acc:P38606]" 2.99562 0.23786762
ATP6V1B1 1759 0.299765 "VACUOLAR ATP SYNTHASE SUBUNIT B, KIDNEY ISOFORM (EC 3.6.3.14) (V- ATPASE B1 SUBUNIT) (VACUOLAR PROTON PUMP B ISOFORM 1) (ENDOMEMBRANE PROTON PUMP 58 KDA SUBUNIT). [SWISSPROT;Acc:P15313]" 1.26636 0.236713889
ATP6V1B2 1744 0.357744 "VACUOLAR ATP SYNTHASE SUBUNIT B, BRAIN ISOFORM (EC 3.6.3.14) (V-ATPASE B2 SUBUNIT) (VACUOLAR PROTON PUMP B ISOFORM 2) (ENDOMEMBRANE PROTON PUMP 58 KDA SUBUNIT) (HO57). [SWISSPROT;Acc:P21281]" 1.51127 0.236717463
ATP6V1D 1749 0.518099 VACUOLAR ATP SYNTHASE SUBUNIT D (EC 3.6.3.14) (V-ATPASE D SUBUNIT) (VACUOLAR PROTON PUMP D SUBUNIT) (V-ATPASE 28 KDA ACCESSORY PROTEIN). [SWISSPROT;Acc:Q9Y5K8] 2.18869 0.236716483
ATP6V1E1 1747 0.480242 VACUOLAR ATP SYNTHASE SUBUNIT E (EC 3.6.3.14) (V-ATPASE E SUBUNIT) (VACUOLAR PROTON PUMP E SUBUNIT) (V-ATPASE 31 KDA SUBUNIT) (P31). [SWISSPROT;Acc:P36543] 2.02876 0.236717009
ATP6V1E2 1757 0.420128 1.77482 0.236715836
ATP6V1F 1760 0.424679 VACUOLAR ATP SYNTHASE SUBUNIT F (EC 3.6.3.14) (V-ATPASE F SUBUNIT) (VACUOLAR PROTON PUMP F SUBUNIT) (V-ATPASE 14 KDA SUBUNIT). [SWISSPROT;Acc:Q16864] 1.79432 0.236679634
ATP6V1G1 1756 0.063055 VACUOLAR ATP SYNTHASE SUBUNIT G 1 (EC 3.6.3.14) (V-ATPASE G SUBUNIT 1) (VACUOLAR PROTON PUMP G SUBUNIT 1) (V-ATPASE 13 KDA SUBUNIT 1) (VACUOLAR ATP SYNTHASE SUBUNIT M16). [SWISSPROT;Acc:O75348] 0.266374 0.236716046
ATP6V1G3 1754 0.0486762 VACUOLAR ATP SYNTHASE SUBUNIT G 3 (EC 3.6.3.14) (V-ATPASE G SUBUNIT 3) (VACUOLAR PROTON PUMP G SUBUNIT 3) (V-ATPASE 13 KDA SUBUNIT 3). [SWISSPROT;Acc:Q96LB4] 0.205631 0.236716254
ATP6V1H 1750 0.0562476 VACUOLAR ATP SYNTHASE SUBUNIT H (EC 3.6.3.14) (V-ATPASE H SUBUNIT) (VACUOLAR PROTON PUMP H SUBUNIT) (V-ATPASE 50/57 KDA SUBUNITS) (VACUOLAR PROTON PUMP SUBUNIT SFD) (CGI-11). [SWISSPROT;Acc:Q9UI12] 0.237616 0.236716383
ATP7A 1656 0.0806616 COPPER-TRANSPORTING ATPASE 1 (EC 3.6.3.4) (COPPER PUMP 1) (MENKES DISEASE-ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q04656] 0.337708 0.238850131
ATP7B 1661 0.0958705 COPPER-TRANSPORTING ATPASE 2 (EC 3.6.3.4) (COPPER PUMP 2) (WILSON DISEASE-ASSOCIATED PROTEIN). [SWISSPROT;Acc:P35670] 0.401402 0.238839119
ATP9A 764 0.0460867 POTENTIAL PHOSPHOLIPID-TRANSPORTING ATPASE IIA (EC 3.6.1.-). [SWISSPROT;Acc:O75110] 0.174809 0.263640316
ATPAF1 2261 0.0308958 0.138512 0.223055042
ATPAF2 394 0.0993399 ATP SYNTHASE MITOCHONDRIAL F1 COMPLEX ASSEMBLY FACTOR 2. [RefSeq;Acc:NM_145691] 0.356562 0.278604843
ATPBD1C 10 0.271296 PROTEIN X 0004. [RefSeq;Acc:NM_016301] 0.5 0.542592
ATPBD3 1736 0.630807 2.66198 0.236969098
ATPBD4 1513 0.0884483 0.36491 0.242383875
ATPIF1 441 0.0602832 "ATPASE INHIBITOR, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:Q9UII2]" 0.217862 0.276703601
ATXN2L 2800 0.070265 ATAXIN 2 RELATED PROTEIN ISOFORM A; ATAXIN-2 DOMAIN PROTEIN. [RefSeq;Acc:NM_007245] 0.353426 0.198811067
AURKA 1255 0.0366317 SERINE/THREONINE KINASE 6 (EC 2.7.1.37) (SERINE/THREONINE KINASE 15) (AURORA/IPL1-RELATED KINASE 1) (AURORA-RELATED KINASE 1) (HARK1) (AURORA-A) (BREAST-TUMOR-AMPLIFIED KINASE). [SWISSPROT;Acc:O14965] 0.148106 0.247334342
AURKB 1257 0.0285544 SERINE/THREONINE PROTEIN KINASE 12 (EC 2.7.1.37) (AURORA- AND IPL1- LIKE MIDBODY-ASSOCIATED PROTEIN 1) (AIM-1) (AURORA/IPL1-RELATED KINASE 2) (AURORA-RELATED KINASE 2) (STK-1) (AURORA-B). [SWISSPROT;Acc:Q96GD4] 0.115449 0.247333455
AURKC 1254 0.0283804 SERINE/THREONINE PROTEIN KINASE 13 (EC 2.7.1.37) (AURORA/IPL1/EG2 PROTEIN 2) (AURORA/IPL1-RELATED KINASE 3) (AURORA-C). [SWISSPROT;Acc:Q9UQB9] 0.114745 0.247334524
AZIN1 2504 0.174979 ORNITHINE DECARBOXYLASE ANTIZYME INHIBITOR. [SWISSPROT;Acc:O14977] 0.814661 0.214787501
B3GNT1 999 0.036112 "N-ACETYLLACTOSAMINIDE BETA-1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE (EC 2.4.1.149) (POLY-N-ACETYLLACTOSAMINE EXTENSION ENZYME) (I-BETA- 1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE) (IGNT) (UDP-GLCNAC:BETAGAL BETA- 1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE 6). [SWISSP" 0.141665 0.254911234
B9D1 193 0.771001 B9 PROTEIN; LIKELY ORTHOLOG OF MOUSE ENDOTHELIAL PRECURSOR PROTEIN B9. [RefSeq;Acc:NM_015681] 2.3671 0.325715432
B9D2 221 0.535221 1.68161 0.318278911
BAAT 575 0.200205 BILE ACID COENZYME A: AMINO ACID N-ACYLTRANSFERASE; GLYCINE N-CHOLOYLTRANSFERASE. [RefSeq;Acc:NM_001701] 0.740509 0.270361333

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/