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 Gene description Rank measured final expected
Results: HTML CSV LaTeX Showing element 1001 to 1050 of 3206 in total
Hugo
description
Rank
measured
final
expected
DDOST DOLICHYL-DIPHOSPHOOLIGOSACCHARIDE--PROTEIN GLYCOSYLTRANSFERASE 48 KDA SUBUNIT PRECURSOR (EC 2.4.1.119) (OLIGOSACCHARYL TRANSFERASE 48 KDA SUBUNIT) (DDOST 48 KDA SUBUNIT). [SWISSPROT;Acc:P39656] 2999 0.0217044 0.135091869 0.160664
DDX12 DEAD/H (ASP-GLU-ALA-ASP/HIS) BOX POLYPEPTIDE 11; DEAD/H BOX-11 (CHL1-RELATED HELICASE GENE-1); YEAST CHL1 HOMOLOG. [RefSeq;Acc:NM_030655] 2766 0.339171 0.20210404 1.6782
DDX18 ATP-DEPENDENT RNA HELICASE DDX18 (DEAD-BOX PROTEIN 18) (MYC-REGULATED DEAD-BOX PROTEIN) (MRDB). [SWISSPROT;Acc:Q9NVP1] 1419 0.858096 0.243931116 3.51778
DDX20 PROBABLE ATP-DEPENDENT RNA HELICASE DDX20 (DEAD-BOX PROTEIN 20) (DEAD- BOX PROTEIN DP 103) (COMPONENT OF GEMS 3) (GEMIN3). [SWISSPROT;Acc:Q9UHI6] 1478 0.092033 0.242975381 0.378775
DDX24 ATP-DEPENDENT RNA HELICASE DDX24 (DEAD-BOX PROTEIN 24). [SWISSPROT;Acc:Q9GZR7] 1363 0.230116 0.244918638 0.939561
DDX31 DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 31 ISOFORM 1; DEAD/DEXH HELICASE DDX31. [RefSeq;Acc:NM_022779] 1231 0.0254237 0.247782272 0.102605
DDX39 "DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 39 ISOFORM 1; NUCLEAR RNA HELICASE, DECD VARIANT OF DEAD BOX FAMILY. [RefSeq;Acc:NM_005804]" 1758 0.0299559 0.236715713 0.126548
DDX4 DEAD-BOX PROTEIN 4 (VASA HOMOLOG). [SWISSPROT;Acc:Q9NQI0] 1223 0.0678848 0.248016338 0.273711
DDX43 DEAD-BOX PROTEIN. [RefSeq;Acc:NM_018665] 2972 0.0292681 0.140309305 0.208597
DDX52 ATP-DEPENDENT RNA HELICASE ROK1; ATP-DEPENDENT RNA HELICASE. [RefSeq;Acc:NM_007010] 1531 0.0764864 0.242218035 0.315775
DDX54 ATP-DEPENDENT RNA HELICASE MGC2835; ATP-DEPENDENT RNA HELICASE; APOPTOSIS RELATED PROTEIN APR-5; DEAD BOX HELICASE 97 KDA. [RefSeq;Acc:NM_024072] 1317 0.517911 0.245660361 2.10824
DDX55 1382 0.191835 0.24462572 0.784198
DDX56 PROBABLE ATP-DEPENDENT 61 KDA NUCLEOLAR RNA HELICASE (DEAD-BOX PROTEIN 21). [SWISSPROT;Acc:Q9NY93] 1329 0.280718 0.245451525 1.14368
DDX6 PROBABLE ATP-DEPENDENT RNA HELICASE P54 (ONCOGENE RCK) (DEAD-BOX PROTEIN 6). [SWISSPROT;Acc:P26196] 2865 0.801671 0.188940556 4.24298
DEAF1 DEFORMED EPIDERMAL AUTOREGULATORY FACTOR 1 HOMOLOG (NUCLEAR DEAF-1 RELATED TRANSCRIPTIONAL REGULATOR) (NUDR) (SUPPRESSIN) (ZINC FINGER MYND DOMAIN CONTAINING PROTEIN 5). [SWISSPROT;Acc:O75398] 1464 0.0656459 0.24303035 0.270114
DEGS1 SPHINGOLIPID DELTA 4 DESATURASE; MEMBRANE FATTY ACID (LIPID) DESATURASE; DIHYDROCERAMIDE DESATURASE. [RefSeq;Acc:NM_003676] 978 0.0374644 0.25535668 0.146714
DENR DENSITY-REGULATED PROTEIN (DRP) (DRP1 PROTEIN) (SMOOTH MUSCLE CELL ASSOCIATED PROTEIN-3) (SMAP-3). [SWISSPROT;Acc:O43583] 2028 0.469395 0.230297663 2.03821
DEPDC5 1669 0.0415385 0.238773668 0.173966
DFFA DNA FRAGMENTATION FACTOR ALPHA SUBUNIT (DNA FRAGMENTATION FACTOR 45 KDA SUBUNIT) (DFF-45) (INHIBITOR OF CAD) (ICAD). [SWISSPROT;Acc:O00273] 1817 0.0764303 0.234266965 0.326253
DFFB DNA FRAGMENTATION FACTOR 40 KDA SUBUNIT (EC 3.-.-.-) (DFF-40) (CASPASE-ACTIVATED DEOXYRIBONUCLEASE) (CASPASE-ACTIVATED DNASE) (CAD) (CASPASE-ACTIVATED NUCLEASE) (CPAN). [SWISSPROT;Acc:O76075] 1821 0.153292 0.234266424 0.654349
DGCR14 DGCR14 PROTEIN (DIGEORGE SYNDROME CRITICAL REGION 14) (ES2 PROTEIN). [SWISSPROT;Acc:Q96DF8] 3100 0.0506529 0.093016709 0.544557
DHDDS DEHYDRODOLICHYL DIPHOSPHATE SYNTHASE. [RefSeq;Acc:NM_024887] 2491 0.238591 0.215618956 1.10654
DHDH DIMERIC DIHYDRODIOL DEHYDROGENASE; 3-DEOXYGLUCOSONE REDUCTASE. [RefSeq;Acc:NM_014475] 1792 0.0986496 0.234884474 0.419992
DHODH "DIHYDROOROTATE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.3.3.1) (DIHYDROOROTATE OXIDASE) (DHODEHASE) (FRAGMENT). [SWISSPROT;Acc:Q02127]" 2269 0.314489 0.222740118 1.41191
DHPS DEOXYHYPUSINE SYNTHASE (EC 2.5.1.46) (DHS). [SWISSPROT;Acc:P49366] 1005 0.138205 0.254818702 0.542366
DHRS7B 567 0.136702 0.270715792 0.504965
DHX15 PUTATIVE PRE-MRNA SPLICING FACTOR RNA HELICASE (DEAH BOX PROTEIN 15) (ATP-DEPENDENT RNA HELICASE #46). [SWISSPROT;Acc:O43143] 408 0.603245 0.278125101 2.16897
DHX35 PROBABLE ATP-DEPENDENT HELICASE DDX35 (DEAH-BOX PROTEIN 35). [SWISSPROT;Acc:Q9H5Z1] 2613 0.0258274 0.211332766 0.122212
DIMT1L "PROBABLE DIMETHYLADENOSINE TRANSFERASE (EC 2.1.1.-) (S- ADENOSYLMETHIONINE-6-N',N'-ADENOSYL(RRNA) DIMETHYLTRANSFERASE) (18S RRNA DIMETHYLASE). [SWISSPROT;Acc:Q9UNQ2]" 1722 0.367472 0.237161334 1.54946
DIP2B SIMILAR TO CG7020 GENE PRODUCT (FRAGMENT). [SPTREMBL;Acc:Q96IB4] 2709 0.465778 0.207346964 2.24637
DIRAS1 SMALL GTP-BINDING TUMOR SUPPRESSOR 1. [RefSeq;Acc:NM_145173] 252 0.168031 0.311889329 0.538752
DIRAS2 DI-RAS2. [RefSeq;Acc:NM_017594] 253 0.210781 0.311887876 0.675823
DKC1 DYSKERIN (NUCLEOLAR PROTEIN NAP57) (CBF5 HOMOLOG). [SWISSPROT;Acc:O60832] 2603 0.95535 0.212026251 4.50581
DLAT "DIHYDROLIPOAMIDE ACETYLTRANSFERASE COMPONENT OF PYRUVATE DEHYDROGENASE COMPLEX, MITOCHONDRIAL PRECURSOR (EC 2.3.1.12) (E2) (PDC-E2) (70 KDA MITOCHONDRIAL AUTOANTIGEN OF PRIMARY BILIARY CIRRHOSIS) (PBC) (M2 ANTIGEN COMPLEX 70 KDA SUBUNIT). [SWISSPRO" 2194 0.607431 0.226018314 2.68753
DLC1 RHO-GTPASE-ACTIVATING PROTEIN 7 (RHO-TYPE GTPASE-ACTIVATING PROTEIN 7) (DELETED IN LIVER CANCER 1 PROTEIN) (DLC-1) (HP PROTEIN) (STAR-RELATED LIPID TRANSFER PROTEIN 12) (STARD12) (START DOMAIN-CONTAINING PROTEIN 12). [SWISSPROT;Acc:Q96QB1] 2621 0.0241725 0.210000261 0.115107
DLD "DIHYDROLIPOAMIDE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.8.1.4) (GLYCINE CLEAVAGE SYSTEM L PROTEIN). [SWISSPROT;Acc:P09622]" 1774 0.596138 0.23591767 2.52689
DLG1 "PRESYNAPTIC PROTEIN SAP97 (SYNAPSE-ASSOCIATED PROTEIN 97) (DISCS, LARGE HOMOLOG 1) (HDLG). [SWISSPROT;Acc:Q12959]" 865 0.16564 0.260284327 0.636381
DLG2 "CHANNEL ASSOCIATED PROTEIN OF SYNAPSE-110 (CHAPSYN-110) (DISCS, LARGE HOMOLOG 2). [SWISSPROT;Acc:Q15700]" 866 0.141754 0.260273394 0.544635
DLG3 "PRESYNAPTIC PROTEIN SAP102 (SYNAPSE-ASSOCIATED PROTEIN 102) (NEUROENDOCRINE-DLG) (NE-DLG) (DISCS, LARGE HOMOLOG 3). [SWISSPROT;Acc:Q92796]" 867 0.138045 0.260272216 0.530387
DLG4 "PRESYNAPTIC DENSITY PROTEIN 95 (PSD-95) (DISCS, LARGE HOMOLOG 4) (POSTSYNAPTIC DENSITY-95). [SWISSPROT;Acc:P78352]" 868 0.138678 0.260271762 0.53282
DLGAP1 DISKS LARGE-ASSOCIATED PROTEIN 1 (DAP-1) (GUANYLATE KINASE-ASSOCIATED PROTEIN) (HGKAP) (SAP90/PSD-95-ASSOCIATED PROTEIN 1) (SAPAP1) (PSD- 95/SAP90 BINDING PROTEIN 1). [SWISSPROT;Acc:O14490] 56 0.378587 0.411154999 0.920789
DLGAP3 DISKS LARGE-ASSOCIATED PROTEIN 3 (DAP-3) (SAP90/PSD-95-ASSOCIATED PROTEIN 3) (SAPAP3) (PSD-95/SAP90 BINDING PROTEIN 3) (FRAGMENT). [SWISSPROT;Acc:O95886] 59 0.28264 0.41115459 0.68743
DLGAP4 DISKS LARGE-ASSOCIATED PROTEIN 4 (DAP-4) (SAP90/PSD-95-ASSOCIATED PROTEIN 4) (SAPAP4) (PSD-95/SAP90 BINDING PROTEIN 4). [SWISSPROT;Acc:Q9Y2H0] 57 0.378587 0.411154999 0.920789
DLSTP "DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX, MITOCHONDRIAL PRECURSOR (EC 2.3.1.61) (E2) (E2K). [SWISSPROT;Acc:P36957]" 1768 0.660595 0.23600433 2.79908
DLX2 HOMEOBOX PROTEIN DLX-2. [SWISSPROT;Acc:Q07687] 2287 0.0581957 0.222342486 0.261739
DLX3 HOMEOBOX PROTEIN DLX-3. [SWISSPROT;Acc:O60479] 2298 0.0439756 0.222341544 0.197784
DLX5 HOMEOBOX PROTEIN DLX-5. [SWISSPROT;Acc:P56178] 2290 0.0443146 0.222342304 0.199308
DMC1 MEIOTIC RECOMBINATION PROTEIN DMC1/LIM15 HOMOLOG. [SWISSPROT;Acc:Q14565] 2343 0.108234 0.220700596 0.490411
DNAJB1 DNAJ HOMOLOG SUBFAMILY B MEMBER 1 (HEAT SHOCK 40 KDA PROTEIN 1) (HEAT SHOCK PROTEIN 40) (HSP40) (DNAJ PROTEIN HOMOLOG 1) (HDJ-1). [SWISSPROT;Acc:P25685] 972 0.0597214 0.255558218 0.23369
DNAJB11 DNAJ HOMOLOG SUBFAMILY B MEMBER 11 PRECURSOR (ER-ASSOCIATED DNAJ PROTEIN 3) (ERJ3) (ER-ASSOCIATED HSP40 CO-CHAPERONE) (HDJ9) (PWP1- INTERACTING PROTEIN 4). [SWISSPROT;Acc:Q9UBS4] 162 0.0661546 0.345685889 0.191372

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/