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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Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 1208 to 1257 of 3206 in total
Rank
description
measured
expected
final
Hugo
1208 RNA-BINDING PROTEIN NOVA-1 (NEURO-ONCOLOGICAL VENTRAL ANTIGEN 1) (ONCONEURAL VENTRAL ANTIGEN-1) (PARANEOPLASTIC RI ANTIGEN) (VENTRAL NEURON-SPECIFIC PROTEIN 1). [SWISSPROT;Acc:P51513] 0.107742 0.434244 0.248113964 NOVA1
1209 DYSTROBREVIN BETA (BETA-DYSTROBREVIN) (DTN-B). [SWISSPROT;Acc:O60941] 0.86712 3.49509 0.248096616 DTNB
1210 "BETA-2-SYNTROPHIN (59 KDA DYSTROPHIN-ASSOCIATED PROTEIN A1, BASIC COMPONENT 2) (SYNTROPHIN 3) (SNT3) (SYNTROPHIN-LIKE) (SNTL). [SWISSPROT;Acc:Q13425]" 0.0666089 0.26852 0.248059362 SNTB2
1211 ANGIOMOTIN LIKE 2; LEMAN COILED-COIL PROTEIN; ANGIOMOTIN-LIKE PROTEIN 2. [RefSeq;Acc:NM_016201] 0.064293 0.259184 0.248059294 AMOTL2
1212 "LIPOAMIDE ACYLTRANSFERASE COMPONENT OF BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE COMPLEX, MITOCHONDRIAL PRECURSOR (EC 2.3.1.-) (E2) (DIHYDROLIPOAMIDE BRANCHED CHAIN TRANSACYLASE) (BCKAD E2 SUBUNIT). [SWISSPROT;Acc:P11182]" 0.121426 0.489504 0.24805926 DBT
1213 DYSTROPHIN. [SWISSPROT;Acc:P11532] 0.0802494 0.323509 0.24805925 no value
1214 ANGIOMOTIN. [RefSeq;Acc:NM_133265] AMOT
1215 "BETA-1-SYNTROPHIN (59 KDA DYSTROPHIN-ASSOCIATED PROTEIN A1, BASIC COMPONENT 1) (DAPA1B) (TAX INTERACTION PROTEIN 43) (TIP-43) (SYNTROPHIN 2) (BSYN2). [SWISSPROT;Acc:Q13884]" SNTB1
1216 NITRILASE 1. [RefSeq;Acc:NM_005600] NIT1
1217 UTROPHIN (DYSTROPHIN-RELATED PROTEIN 1) (DRP1) (DRP). [SWISSPROT;Acc:P46939] 0.0621046 0.250362 0.24805921 UTRN
1218 "ALPHA-1-SYNTROPHIN (59 KDA DYSTROPHIN-ASSOCIATED PROTEIN A1, ACIDIC COMPONENT 1) (PRO-TGF-ALPHA CYTOPLASMIC DOMAIN-INTERACTING PROTEIN 1) (TACIP1) (SYNTROPHIN 1). [SWISSPROT;Acc:Q13424]" 0.0640593 0.258242 0.248059185 SNTA1
1219 0.0424937 0.171305 0.248058726 WDR55
1220 PESCADILLO HOMOLOG 1. [SWISSPROT;Acc:O00541] 0.913889 3.68475 0.248019269 PES1
1221 VISININ-LIKE PROTEIN 3 (VILIP-3) (CALCIUM-BINDING PROTEIN BDR-1) (HLP2) (HIPPOCALCIN-LIKE PROTEIN 1). [SWISSPROT;Acc:P37235] 0.179279 0.722847 0.248017907 HPCAL1
1222 DYSTROBREVIN ALPHA (DYSTROBREVIN-ALPHA). [SWISSPROT;Acc:Q9Y4J8] 0.762918 3.07607 0.248017113 DTNA
1223 DEAD-BOX PROTEIN 4 (VASA HOMOLOG). [SWISSPROT;Acc:Q9NQI0] 0.0678848 0.273711 0.248016338 DDX4
1224 NEURON SPECIFIC CALCIUM-BINDING PROTEIN HIPPOCALCIN (P23K) (CALCIUM- BINDING PROTEIN BDR-2). [SWISSPROT;Acc:P32076] 0.150518 0.606896 0.248012839 HPCA
1225 NEUROCALCIN DELTA. [SWISSPROT;Acc:P29554] 0.14688 0.592229 0.248012171 NCALD
1226 1.12354 4.53144 0.247943259 KIAA0020
1227 SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN C1; MAMMALIAN CHROMATIN REMODELING COMPLEX BRG1-ASSOCIATED FACTOR 155; SWI/SNF COMPLEX 155 KDA SUBUNIT; CHROMATIN REMODELING COMPLEX BAF155 SUBUNIT. [RefSeq;Acc:NM_003074] 0.720529 2.90646 0.247906044 SMARCC1
1228 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN M (HNRNP M). [SWISSPROT;Acc:P52272] 0.266011 1.07305 0.247901775 HNRPM
1229 ARF GTPASE-ACTIVATING PROTEIN GIT2 (G PROTEIN-COUPLED RECEPTOR KINASE- INTERACTOR 2). [SWISSPROT;Acc:Q14161] 0.345758 1.39492 0.247869412 GIT2
1230 0.6803 2.74555 0.247782776 RRP12
1231 DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 31 ISOFORM 1; DEAD/DEXH HELICASE DDX31. [RefSeq;Acc:NM_022779] 0.0254237 0.102605 0.247782272 DDX31
1232 0.0836052 0.33749 0.247726451 KIAA0859
1233 POLYBROMO 1. [RefSeq;Acc:NM_018165] 0.128218 0.517633 0.247700591 PBRM1
1234 POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L2 (SNF2-ALPHA). [SWISSPROT;Acc:P51531] 0.130458 0.526678 0.247699733 SMARCA2
1235 POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L4 (SNF2-BETA) (BRG-1 PROTEIN) (MITOTIC GROWTH AND TRANSCRIPTION ACTIVATOR) (BRAHMA PROTEIN HOMOLOG 1). [SWISSPROT;Acc:P51532] SMARCA4
1236 POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L1. [SWISSPROT;Acc:P28370] 0.271278 1.09519 0.247699486 SMARCA1
1237 SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN A5; SUCROSE NONFERMENTING-LIKE 5. [RefSeq;Acc:NM_003601] 0.307072 1.2397 0.247698637 SMARCA5
1238 TBP-ASSOCIATED FACTOR 172 (TAF-172) (TAF(II)170). [SWISSPROT;Acc:O14981] 0.283008 1.14255 0.247698569 BTAF1
1239 "POTASSIUM VOLTAGE-GATED CHANNEL, SHAL-RELATED SUBFAMILY, MEMBER 1; SHAL-TYPE POTASSIUM CHANNEL; VOLTAGE-GATED POTASSIUM CHANNEL KV4.1. [RefSeq;Acc:NM_004979]" 0.280939 1.13458 0.247614976 KCND1
1240 "POTASSIUM VOLTAGE-GATED CHANNEL, SHAL-RELATED SUBFAMILY, MEMBER 3 ISOFORM 1; SHA1-RELATED POTASSIUM CHANNEL KV4.3; VOLTAGE-GATED K+ CHANNEL; POTASSIUM IONIC CHANNEL KV4.3; VOLTAGE-GATED POTASSIUM CHANNEL KV4.3. [RefSeq;Acc:NM_004980]" 0.307623 1.24236 0.247611803 KCND3
1241 0.288556 1.16536 0.247611039 C22orf25
1242 CYSTATHIONINE GAMMA-LYASE (EC 4.4.1.1) (GAMMA-CYSTATHIONASE). [SWISSPROT;Acc:P32929] 0.0790456 0.319234 0.247610217 CTH
1243 "POTASSIUM VOLTAGE-GATED CHANNEL, SHAL-RELATED SUBFAMILY, MEMBER 2; VOLTAGE-SENSITIVE POTASSIUM CHANNEL; VOLTAGE-GATED POTASSIUM CHANNEL KV4.2. [RefSeq;Acc:NM_012281]" 0.363365 1.46751 0.24760649 KCND2
1244 "SOLUTE CARRIER FAMILY 2, FACILITATED GLUCOSE TRANSPORTER, MEMBER 6 (GLUCOSE TRANSPORTER TYPE 6) (GLUCOSE TRANSPORTER TYPE 9). [SWISSPROT;Acc:Q9UGQ3]" 0.0527752 0.213145 0.247602336 SLC2A6
1245 "SOLUTE CARRIER FAMILY 2, FACILITATED GLUCOSE TRANSPORTER, MEMBER 8 (GLUCOSE TRANSPORTER TYPE 8) (GLUCOSE TRANSPORTER TYPE X1). [SWISSPROT;Acc:Q9NY64]" 0.069385 0.280228 0.247601953 SLC2A8
1246 DNA-DIRECTED RNA POLYMERASE II 16 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB4). [SWISSPROT;Acc:O15514] 0.139566 0.563754 0.247565427 POLR2D
1247 FIBRILLARIN (34 KDA NUCLEOLAR SCLERODERMA ANTIGEN). [SWISSPROT;Acc:P22087] 1.27878 5.16557 0.247558353 FBL
1248 SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN C2 ISOFORM A; MAMMALIAN CHROMATIN REMODELING COMPLEX BRG1-ASSOCIATED FACTOR 170; CHROMATIN REMODELING COMPLEX BAF170 SUBUNIT; SWI3-LIKE PROTEIN; SWI/SNF COMPLEX 170 KDA SUBUNIT. [Sou 0.66815 2.69939 0.247518884 SMARCC2
1249 60S ACIDIC RIBOSOMAL PROTEIN P0 (L10E). [SWISSPROT;Acc:P05388] 0.11779 0.476127 0.247391977 RPLP0
1250 BLOCK 23. [SPTREMBL;Acc:Q8NHW5] 0.11539 0.46643 0.247389748 no value
1251 "SIMILAR TO RIBOSOMAL PROTEIN, LARGE, P0. [SPTREMBL;Acc:Q96FQ9]" 0.100674 0.406955 0.247383617
1252 METHYLENETETRAHYDROFOLATE REDUCTASE (EC 1.5.1.20). [SWISSPROT;Acc:P42898] 0.121247 0.490121 0.247381769 MTHFR
1253 IMPORTIN 4. [RefSeq;Acc:NM_024658] 0.572386 2.31408 0.247349271 no value
1254 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] 0.0283804 0.114745 0.247334524 AURKC
1255 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] 0.0366317 0.148106 0.247334342 AURKA
1256 "CYLINDROMATOSIS (TURBAN TUMOR SYNDROME); CYLINDROMATOSIS 1, TURBAN TUMOR SYNDROME. [RefSeq;Acc:NM_015247]" CYLD
1257 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] 0.0285544 0.115449 0.247333455 AURKB

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/