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 [...,...].
Gene expected Rank description measured final Hugo
Results: HTML CSV LaTeX Showing element 1702 to 1751 of 3206 in total
expected
Rank
description
measured
final
Hugo
0.581157 2546 "CYTOCHROME C OXIDASE ASSEMBLY PROTEIN COX11, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:Q9Y6N1]" 0.124724 0.214613263 COX11
0.582135 163 NUCLEAR PROTEIN UKP68. [RefSeq;Acc:NM_024824] 0.200368 0.344195075 ZC3H14
0.582446 1037 LOH1CR12. [RefSeq;Acc:NM_058169] 0.147556 0.253338507 LOH12CR1
0.583751 1277 MAGUK P55 SUBFAMILY MEMBER 6 (VELI-ASSOCIATED MAGUK 1) (VAM-1). [SWISSPROT;Acc:Q9NZW5] 0.143838 0.246403004 MPP6
0.584621 837 0.152414 0.260705654 SLC46A1
838 SLC46A3
0.584702 2653 NUMB-LIKE PROTEIN (NUMB-R). [SWISSPROT;Acc:Q9Y6R0] 0.122765 0.209961656 NUMBL
0.584848 2064 0.134261 0.229565631 GPD1L
0.58514 1307 PROTEIN DISULFIDE ISOMERASE PRECURSOR (PDI) (EC 5.3.4.1) (PROLYL 4- HYDROXYLASE BETA SUBUNIT) (CELLULAR THYROID HORMONE BINDING PROTEIN) (P55). [SWISSPROT;Acc:P07237] 0.143784 0.245725809 P4HB
0.585616 156 0.205566 0.351025245 DTX4
0.586832 2693 0.122185 0.208211209 AIFM3
0.586856 977 TSC22-RELATED INDUCIBLE LEUCINE ZIPPER PROTEIN 2 (TSC-22-LIKE PROTEIN THG-1). [SWISSPROT;Acc:Q9Y3Q8] 0.149858 0.255357362 TSC22D4
0.587107 3096 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-8 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-8 SUBUNIT). [SWISSPROT;Acc:Q8WXS5] 0.0570584 0.097185692 CACNG8
3097 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-3 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-3 SUBUNIT). [SWISSPROT;Acc:O60359] CACNG3
0.587298 886 KINESIN HEAVY CHAIN ISOFORM 5C (KINESIN HEAVY CHAIN NEURON-SPECIFIC 2). [SWISSPROT;Acc:O60282] 0.152626 0.25987829 KIF5C
0.587978 3095 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-2 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-2 SUBUNIT). [SWISSPROT;Acc:Q9Y698] 0.0571433 0.097186119 CACNG2
0.589168 3085 DEOXYRIBONUCLEASE II BETA ISOFORM 1 PRECURSOR; DEOXYRIBONUCLEASE II BETA; ENDONUCLEASE DLAD. [RefSeq;Acc:NM_021233] 0.0586001 0.099462462 DNASE2B
0.589242 95 POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 2 (POTASSIUM CHANNEL KV1.2) (RBK2) (HBK5) (NGK1) (MK2) (HUKIV). [SWISSPROT;Acc:P16389] 0.22158 0.376042441 KCNA2
0.590154 3094 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-4 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-4 SUBUNIT). [SWISSPROT;Acc:Q9UBN1] 0.0573556 0.097187514 CACNG4
0.590289 1052 ANNEXIN A7 (ANNEXIN VII) (SYNEXIN). [SWISSPROT;Acc:P20073] 0.149169 0.252705031 ANXA7
0.591312 676 "TRYPTOPHAN 2,3-DIOXYGENASE (EC 1.13.11.11) (TRYPTOPHAN PYRROLASE) (TRYPTOPHANASE) (TRYPTOPHAN OXYGENASE) (TRYPTAMIN 2,3-DIOXYGENASE) (TRPO). [SWISSPROT;Acc:P48775]" 0.157338 0.26608288 TDO2
0.591632 2272 "GLYCEROL KINASE, TESTIS SPECIFIC 1 (EC 2.7.1.30) (ATP:GLYCEROL 3- PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:Q14409]" 0.131767 0.222717838 no value
0.59173 1185 "ACTIVIN A RECEPTOR, TYPE IC; ACTIVIN RECEPTOR-LIKE KINASE 7. [RefSeq;Acc:NM_145259]" 0.147145 0.248669157 ACVR1C
0.592229 1225 NEUROCALCIN DELTA. [SWISSPROT;Acc:P29554] 0.14688 0.248012171 NCALD
0.5927 1196 DIHYDROPYRIMIDINE DEHYDROGENASE [NADP+] PRECURSOR (EC 1.3.1.2) (DPD) (DHPDHASE) (DIHYDROURACIL DEHYDROGENASE) (DIHYDROTHYMINE DEHYDROGENASE). [SWISSPROT;Acc:Q12882] 0.147283 0.248495023 no value
0.593022 2664 DEOXYCYTIDYLATE DEAMINASE (EC 3.5.4.12) (DCMP DEAMINASE). [SWISSPROT;Acc:P32321] 0.124149 0.209349737 DCTD
0.593047 1357 ELONGATION FACTOR 1-ALPHA 2 (EF-1-ALPHA-2) (ELONGATION FACTOR 1 A-2) (EEF1A-2) (STATIN S1). [SWISSPROT;Acc:Q05639] 0.145347 0.245085128 EEF1A2
0.595639 1323 CENTROMERE PROTEIN J; CENTROSOMAL P4.1-ASSOCIATED PROTEIN; LYST-INTERACTING PROTEIN LIP1; LAG-3-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_018451] 0.146257 0.24554638 CENPJ
0.598119 1358 ELONGATION FACTOR 1-ALPHA 1 (EF-1-ALPHA-1) (ELONGATION FACTOR 1 A-1) (EEF1A-1) (ELONGATION FACTOR TU) (EF-TU). [SWISSPROT;Acc:P04720] 0.14659 0.245085008 EEF1AL3
0.598643 2559 0.128297 0.214313038 CEP164
0.598798 1625 PROTEIN KINASE PKX1 (EC 2.7.1.-). [SWISSPROT;Acc:P51817] 0.143332 0.239366197 PRKX
0.600397 1030 RETINOBLASTOMA-LIKE PROTEIN 2 (130 KDA RETINOBLASTOMA-ASSOCIATED PROTEIN) (PRB2) (P130) (RBR-2). [SWISSPROT;Acc:Q08999] 0.152107 0.253344037 RBL2
0.600447 682 CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II BETA CHAIN (EC 2.7.1.123) (CAM-KINASE II BETA CHAIN) (CAM KINASE II BETA SUBUNIT) (CAMK-II BETA SUBUNIT). [SWISSPROT;Acc:Q13554] 0.159505 0.265643762 CAMK2B
683 CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN (EC 2.7.1.123) (CAM-KINASE II DELTA CHAIN) (CAM KINASE II DELTA SUBUNIT) (CAMK-II DELTA SUBUNIT). [SWISSPROT;Acc:Q13557] CAMK2D
0.60095 2396 SQUALENE MONOOXYGENASE (EC 1.14.99.7) (SQUALENE EPOXIDASE) (SE). [SWISSPROT;Acc:Q14534] 0.131761 0.219254514 SQLE
0.601521 204 CARNITINE O-ACETYLTRANSFERASE (EC 2.3.1.7) (CARNITINE ACETYLASE) (CAT). [SWISSPROT;Acc:P43155] 0.193666 0.321960497 CRAT
0.601543 143 GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-1 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P14867] 0.211371 0.351381364 GABRA1
0.601708 1135 PROTEASOME SUBUNIT BETA TYPE 7 PRECURSOR (EC 3.4.25.1) (PROTEASOME SUBUNIT Z) (MACROPAIN CHAIN Z) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX CHAIN Z). [SWISSPROT;Acc:Q99436] 0.150695 0.250445399 PSMB7
0.601977 2913 CYTOSKELETON RELATED VITAMIN A RESPONSIVE PROTEIN; GLUTAMATE TRANSPORTER EEAC1-ASSOCIATED PROTEIN; DERMAL PAPILLA DERIVED PROTEIN 11; PUTATIVE MAPK ACTIVATING PROTEIN PM27. [RefSeq;Acc:NM_006407] 0.104678 0.173890365 ARL6IP5
0.602532 144 GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-2 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P47869] 0.211718 0.351380508 GABRA2
0.603029 699 0.160096 0.265486403 USP47
0.603475 1372 HISTONE H3.4 (H3T) (H3/T) (H3/G). [SWISSPROT;Acc:Q16695] 0.147768 0.244861842 HIST3H3
0.60397 2397 KYNURENINE 3-MONOOXYGENASE (KYNURENINE 3-HYDROXYLASE). [RefSeq;Acc:NM_003679] 0.132423 0.219254268 KMO
2398 UBIQUINONE BIOSYNTHESIS MONOOXGENASE COQ6 (EC 1.14.13.-) (CGI-10). [SWISSPROT;Acc:Q9Y2Z9] COQ6
0.604755 141 GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-3 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P34903] 0.2125 0.351381965 GABRA3
0.605166 2616 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 3 (EC 2.7.1.-) (MAP KINASE KINASE 3) (MAPKK 3) (MAPK/ERK KINASE 3). [SWISSPROT;Acc:P46734] 0.127536 0.210745481 MAP2K3
0.605241 1977 "ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:O76031]" 0.139859 0.231079851 CLPX
0.605534 2335 ADENOSYLHOMOCYSTEINASE (EC 3.3.1.1) (S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE) (ADOHCYASE). [SWISSPROT;Acc:P23526] 0.133936 0.221186589 AHCY
0.605923 1186 SERINE/THREONINE-PROTEIN KINASE RECEPTOR R2 PRECURSOR (EC 2.7.1.37) (SKR2) (ACTIVIN RECEPTOR-LIKE KINASE 4) (ALK-4) (ACTR-IB). [SWISSPROT;Acc:P36896] 0.150674 0.24866856 ACVR1B
0.606896 1224 NEURON SPECIFIC CALCIUM-BINDING PROTEIN HIPPOCALCIN (P23K) (CALCIUM- BINDING PROTEIN BDR-2). [SWISSPROT;Acc:P32076] 0.150518 0.248012839 HPCA

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/