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

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/