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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final Gene expected Rank measured description Hugo
Results: HTML CSV LaTeX Showing element 1952 to 2001 of 3206 in total
final
expected
Rank
measured
description
Hugo
0.247334342 0.148106 1256 0.0366317 "CYLINDROMATOSIS (TURBAN TUMOR SYNDROME); CYLINDROMATOSIS 1, TURBAN TUMOR SYNDROME. [RefSeq;Acc:NM_015247]" CYLD
0.247334524 0.114745 1254 0.0283804 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] AURKC
0.247349271 2.31408 1253 0.572386 IMPORTIN 4. [RefSeq;Acc:NM_024658] no value
0.247381769 0.490121 1252 0.121247 METHYLENETETRAHYDROFOLATE REDUCTASE (EC 1.5.1.20). [SWISSPROT;Acc:P42898] MTHFR
0.247383617 0.406955 1251 0.100674 "SIMILAR TO RIBOSOMAL PROTEIN, LARGE, P0. [SPTREMBL;Acc:Q96FQ9]" no value
0.247389748 0.46643 1250 0.11539 BLOCK 23. [SPTREMBL;Acc:Q8NHW5]
0.247391977 0.476127 1249 0.11779 60S ACIDIC RIBOSOMAL PROTEIN P0 (L10E). [SWISSPROT;Acc:P05388] RPLP0
0.247518884 2.69939 1248 0.66815 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 SMARCC2
0.247558353 5.16557 1247 1.27878 FIBRILLARIN (34 KDA NUCLEOLAR SCLERODERMA ANTIGEN). [SWISSPROT;Acc:P22087] FBL
0.247565427 0.563754 1246 0.139566 DNA-DIRECTED RNA POLYMERASE II 16 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB4). [SWISSPROT;Acc:O15514] POLR2D
0.247601953 0.280228 1245 0.069385 "SOLUTE CARRIER FAMILY 2, FACILITATED GLUCOSE TRANSPORTER, MEMBER 8 (GLUCOSE TRANSPORTER TYPE 8) (GLUCOSE TRANSPORTER TYPE X1). [SWISSPROT;Acc:Q9NY64]" SLC2A8
0.247602336 0.213145 1244 0.0527752 "SOLUTE CARRIER FAMILY 2, FACILITATED GLUCOSE TRANSPORTER, MEMBER 6 (GLUCOSE TRANSPORTER TYPE 6) (GLUCOSE TRANSPORTER TYPE 9). [SWISSPROT;Acc:Q9UGQ3]" SLC2A6
0.24760649 1.46751 1243 0.363365 "POTASSIUM VOLTAGE-GATED CHANNEL, SHAL-RELATED SUBFAMILY, MEMBER 2; VOLTAGE-SENSITIVE POTASSIUM CHANNEL; VOLTAGE-GATED POTASSIUM CHANNEL KV4.2. [RefSeq;Acc:NM_012281]" KCND2
0.247610217 0.319234 1242 0.0790456 CYSTATHIONINE GAMMA-LYASE (EC 4.4.1.1) (GAMMA-CYSTATHIONASE). [SWISSPROT;Acc:P32929] CTH
0.247611039 1.16536 1241 0.288556 C22orf25
0.247611803 1.24236 1240 0.307623 "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]" KCND3
0.247614976 1.13458 1239 0.280939 "POTASSIUM VOLTAGE-GATED CHANNEL, SHAL-RELATED SUBFAMILY, MEMBER 1; SHAL-TYPE POTASSIUM CHANNEL; VOLTAGE-GATED POTASSIUM CHANNEL KV4.1. [RefSeq;Acc:NM_004979]" KCND1
0.247698569 1.14255 1238 0.283008 TBP-ASSOCIATED FACTOR 172 (TAF-172) (TAF(II)170). [SWISSPROT;Acc:O14981] BTAF1
0.247698637 1.2397 1237 0.307072 SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN A5; SUCROSE NONFERMENTING-LIKE 5. [RefSeq;Acc:NM_003601] SMARCA5
0.247699486 1.09519 1236 0.271278 POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L1. [SWISSPROT;Acc:P28370] SMARCA1
0.247699733 0.526678 1234 0.130458 POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L2 (SNF2-ALPHA). [SWISSPROT;Acc:P51531] 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
0.247700591 0.517633 1233 0.128218 POLYBROMO 1. [RefSeq;Acc:NM_018165] PBRM1
0.247726451 0.33749 1232 0.0836052 KIAA0859
0.247782272 0.102605 1231 0.0254237 DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 31 ISOFORM 1; DEAD/DEXH HELICASE DDX31. [RefSeq;Acc:NM_022779] DDX31
0.247782776 2.74555 1230 0.6803 RRP12
0.247869412 1.39492 1229 0.345758 ARF GTPASE-ACTIVATING PROTEIN GIT2 (G PROTEIN-COUPLED RECEPTOR KINASE- INTERACTOR 2). [SWISSPROT;Acc:Q14161] GIT2
0.247901775 1.07305 1228 0.266011 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN M (HNRNP M). [SWISSPROT;Acc:P52272] HNRPM
0.247906044 2.90646 1227 0.720529 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] SMARCC1
0.247943259 4.53144 1226 1.12354 KIAA0020
0.248012171 0.592229 1225 0.14688 NEUROCALCIN DELTA. [SWISSPROT;Acc:P29554] NCALD
0.248012839 0.606896 1224 0.150518 NEURON SPECIFIC CALCIUM-BINDING PROTEIN HIPPOCALCIN (P23K) (CALCIUM- BINDING PROTEIN BDR-2). [SWISSPROT;Acc:P32076] HPCA
0.248016338 0.273711 1223 0.0678848 DEAD-BOX PROTEIN 4 (VASA HOMOLOG). [SWISSPROT;Acc:Q9NQI0] DDX4
0.248017113 3.07607 1222 0.762918 DYSTROBREVIN ALPHA (DYSTROBREVIN-ALPHA). [SWISSPROT;Acc:Q9Y4J8] DTNA
0.248017907 0.722847 1221 0.179279 VISININ-LIKE PROTEIN 3 (VILIP-3) (CALCIUM-BINDING PROTEIN BDR-1) (HLP2) (HIPPOCALCIN-LIKE PROTEIN 1). [SWISSPROT;Acc:P37235] HPCAL1
0.248019269 3.68475 1220 0.913889 PESCADILLO HOMOLOG 1. [SWISSPROT;Acc:O00541] PES1
0.248058726 0.171305 1219 0.0424937 WDR55
0.248059185 0.258242 1218 0.0640593 "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]" SNTA1
0.24805921 0.250362 1217 0.0621046 UTROPHIN (DYSTROPHIN-RELATED PROTEIN 1) (DRP1) (DRP). [SWISSPROT;Acc:P46939] UTRN
0.24805925 0.323509 1213 0.0802494 DYSTROPHIN. [SWISSPROT;Acc:P11532] 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
0.24805926 0.489504 1212 0.121426 "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]" DBT
0.248059294 0.259184 1211 0.064293 ANGIOMOTIN LIKE 2; LEMAN COILED-COIL PROTEIN; ANGIOMOTIN-LIKE PROTEIN 2. [RefSeq;Acc:NM_016201] AMOTL2
0.248059362 0.26852 1210 0.0666089 "BETA-2-SYNTROPHIN (59 KDA DYSTROPHIN-ASSOCIATED PROTEIN A1, BASIC COMPONENT 2) (SYNTROPHIN 3) (SNT3) (SYNTROPHIN-LIKE) (SNTL). [SWISSPROT;Acc:Q13425]" SNTB2
0.248096616 3.49509 1209 0.86712 DYSTROBREVIN BETA (BETA-DYSTROBREVIN) (DTN-B). [SWISSPROT;Acc:O60941] DTNB
0.248113964 0.434244 1208 0.107742 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] NOVA1
0.248160981 0.443579 1207 0.110079 no value
0.248198093 1.28364 1206 0.318597 LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS). [SWISSPROT;Acc:Q15046] KARS

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/