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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expected Gene measured Rank Hugo description final
Results: HTML CSV LaTeX Showing element 1701 to 1750 of 3206 in total
expected
measured
Rank
Hugo
description
final
0.580932 0.121 2686 EHD1 EH-DOMAIN CONTAINING PROTEIN 1 (TESTILIN) (HPAST1). [SWISSPROT;Acc:Q9H4M9] 0.208285996
0.581157 0.124724 2546 COX11 "CYTOCHROME C OXIDASE ASSEMBLY PROTEIN COX11, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:Q9Y6N1]" 0.214613263
0.582135 0.200368 163 ZC3H14 NUCLEAR PROTEIN UKP68. [RefSeq;Acc:NM_024824] 0.344195075
0.582446 0.147556 1037 LOH12CR1 LOH1CR12. [RefSeq;Acc:NM_058169] 0.253338507
0.583751 0.143838 1277 MPP6 MAGUK P55 SUBFAMILY MEMBER 6 (VELI-ASSOCIATED MAGUK 1) (VAM-1). [SWISSPROT;Acc:Q9NZW5] 0.246403004
0.584621 0.152414 837 SLC46A1 0.260705654
838 SLC46A3
0.584702 0.122765 2653 NUMBL NUMB-LIKE PROTEIN (NUMB-R). [SWISSPROT;Acc:Q9Y6R0] 0.209961656
0.584848 0.134261 2064 GPD1L 0.229565631
0.58514 0.143784 1307 P4HB PROTEIN DISULFIDE ISOMERASE PRECURSOR (PDI) (EC 5.3.4.1) (PROLYL 4- HYDROXYLASE BETA SUBUNIT) (CELLULAR THYROID HORMONE BINDING PROTEIN) (P55). [SWISSPROT;Acc:P07237] 0.245725809
0.585616 0.205566 156 DTX4 0.351025245
0.586832 0.122185 2693 AIFM3 0.208211209
0.586856 0.149858 977 TSC22D4 TSC22-RELATED INDUCIBLE LEUCINE ZIPPER PROTEIN 2 (TSC-22-LIKE PROTEIN THG-1). [SWISSPROT;Acc:Q9Y3Q8] 0.255357362
0.587107 0.0570584 3096 CACNG8 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-8 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-8 SUBUNIT). [SWISSPROT;Acc:Q8WXS5] 0.097185692
3097 CACNG3 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-3 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-3 SUBUNIT). [SWISSPROT;Acc:O60359]
0.587298 0.152626 886 KIF5C KINESIN HEAVY CHAIN ISOFORM 5C (KINESIN HEAVY CHAIN NEURON-SPECIFIC 2). [SWISSPROT;Acc:O60282] 0.25987829
0.587978 0.0571433 3095 CACNG2 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-2 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-2 SUBUNIT). [SWISSPROT;Acc:Q9Y698] 0.097186119
0.589168 0.0586001 3085 DNASE2B DEOXYRIBONUCLEASE II BETA ISOFORM 1 PRECURSOR; DEOXYRIBONUCLEASE II BETA; ENDONUCLEASE DLAD. [RefSeq;Acc:NM_021233] 0.099462462
0.589242 0.22158 95 KCNA2 POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 2 (POTASSIUM CHANNEL KV1.2) (RBK2) (HBK5) (NGK1) (MK2) (HUKIV). [SWISSPROT;Acc:P16389] 0.376042441
0.590154 0.0573556 3094 CACNG4 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-4 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-4 SUBUNIT). [SWISSPROT;Acc:Q9UBN1] 0.097187514
0.590289 0.149169 1052 ANXA7 ANNEXIN A7 (ANNEXIN VII) (SYNEXIN). [SWISSPROT;Acc:P20073] 0.252705031
0.591312 0.157338 676 TDO2 "TRYPTOPHAN 2,3-DIOXYGENASE (EC 1.13.11.11) (TRYPTOPHAN PYRROLASE) (TRYPTOPHANASE) (TRYPTOPHAN OXYGENASE) (TRYPTAMIN 2,3-DIOXYGENASE) (TRPO). [SWISSPROT;Acc:P48775]" 0.26608288
0.591632 0.131767 2272 no value "GLYCEROL KINASE, TESTIS SPECIFIC 1 (EC 2.7.1.30) (ATP:GLYCEROL 3- PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:Q14409]" 0.222717838
0.59173 0.147145 1185 ACVR1C "ACTIVIN A RECEPTOR, TYPE IC; ACTIVIN RECEPTOR-LIKE KINASE 7. [RefSeq;Acc:NM_145259]" 0.248669157
0.592229 0.14688 1225 NCALD NEUROCALCIN DELTA. [SWISSPROT;Acc:P29554] 0.248012171
0.5927 0.147283 1196 no value DIHYDROPYRIMIDINE DEHYDROGENASE [NADP+] PRECURSOR (EC 1.3.1.2) (DPD) (DHPDHASE) (DIHYDROURACIL DEHYDROGENASE) (DIHYDROTHYMINE DEHYDROGENASE). [SWISSPROT;Acc:Q12882] 0.248495023
0.593022 0.124149 2664 DCTD DEOXYCYTIDYLATE DEAMINASE (EC 3.5.4.12) (DCMP DEAMINASE). [SWISSPROT;Acc:P32321] 0.209349737
0.593047 0.145347 1357 EEF1A2 ELONGATION FACTOR 1-ALPHA 2 (EF-1-ALPHA-2) (ELONGATION FACTOR 1 A-2) (EEF1A-2) (STATIN S1). [SWISSPROT;Acc:Q05639] 0.245085128
0.595639 0.146257 1323 CENPJ CENTROMERE PROTEIN J; CENTROSOMAL P4.1-ASSOCIATED PROTEIN; LYST-INTERACTING PROTEIN LIP1; LAG-3-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_018451] 0.24554638
0.598119 0.14659 1358 EEF1AL3 ELONGATION FACTOR 1-ALPHA 1 (EF-1-ALPHA-1) (ELONGATION FACTOR 1 A-1) (EEF1A-1) (ELONGATION FACTOR TU) (EF-TU). [SWISSPROT;Acc:P04720] 0.245085008
0.598643 0.128297 2559 CEP164 0.214313038
0.598798 0.143332 1625 PRKX PROTEIN KINASE PKX1 (EC 2.7.1.-). [SWISSPROT;Acc:P51817] 0.239366197
0.600397 0.152107 1030 RBL2 RETINOBLASTOMA-LIKE PROTEIN 2 (130 KDA RETINOBLASTOMA-ASSOCIATED PROTEIN) (PRB2) (P130) (RBR-2). [SWISSPROT;Acc:Q08999] 0.253344037
0.600447 0.159505 682 CAMK2B 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] 0.265643762
683 CAMK2D 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]
0.60095 0.131761 2396 SQLE SQUALENE MONOOXYGENASE (EC 1.14.99.7) (SQUALENE EPOXIDASE) (SE). [SWISSPROT;Acc:Q14534] 0.219254514
0.601521 0.193666 204 CRAT CARNITINE O-ACETYLTRANSFERASE (EC 2.3.1.7) (CARNITINE ACETYLASE) (CAT). [SWISSPROT;Acc:P43155] 0.321960497
0.601543 0.211371 143 GABRA1 GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-1 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P14867] 0.351381364
0.601708 0.150695 1135 PSMB7 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] 0.250445399
0.601977 0.104678 2913 ARL6IP5 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] 0.173890365
0.602532 0.211718 144 GABRA2 GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-2 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P47869] 0.351380508
0.603029 0.160096 699 USP47 0.265486403
0.603475 0.147768 1372 HIST3H3 HISTONE H3.4 (H3T) (H3/T) (H3/G). [SWISSPROT;Acc:Q16695] 0.244861842
0.60397 0.132423 2397 KMO KYNURENINE 3-MONOOXYGENASE (KYNURENINE 3-HYDROXYLASE). [RefSeq;Acc:NM_003679] 0.219254268
2398 COQ6 UBIQUINONE BIOSYNTHESIS MONOOXGENASE COQ6 (EC 1.14.13.-) (CGI-10). [SWISSPROT;Acc:Q9Y2Z9]
0.604755 0.2125 141 GABRA3 GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-3 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P34903] 0.351381965
0.605166 0.127536 2616 MAP2K3 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] 0.210745481
0.605241 0.139859 1977 CLPX "ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:O76031]" 0.231079851
0.605534 0.133936 2335 AHCY ADENOSYLHOMOCYSTEINASE (EC 3.3.1.1) (S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE) (ADOHCYASE). [SWISSPROT;Acc:P23526] 0.221186589
0.605923 0.150674 1186 ACVR1B 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] 0.24866856

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/