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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Gene Rank expected description measured Hugo final
Results: HTML CSV LaTeX Showing element 1201 to 1250 of 3206 in total
Rank
expected
description
measured
Hugo
final
1201 0.432185 0.107333 FAM40A 0.248349665
1202 0.277567 0.0689331 TMTC4 0.248347606
1203 0.362464 0.0900162 FAM40B 0.248345215
1204 1.15632 KV CHANNEL INTERACTING PROTEIN 1; VESICLE APC-BINDING PROTEIN; A-TYPE POTASSIUM CHANNEL MODULATORY PROTEIN 1. [RefSeq;Acc:NM_014592] 0.287166 KCNIP1 0.248344749
1205 0.525788 ZINC FINGER PROTEIN T86. [SWISSPROT;Acc:O00488] 0.130571 ZNF593 0.248333929
1206 1.28364 LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS). [SWISSPROT;Acc:Q15046] 0.318597 KARS 0.248198093
1207 0.443579 0.110079 no value 0.248160981
1208 0.434244 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 NOVA1 0.248113964
1209 3.49509 DYSTROBREVIN BETA (BETA-DYSTROBREVIN) (DTN-B). [SWISSPROT;Acc:O60941] 0.86712 DTNB 0.248096616
1210 0.26852 "BETA-2-SYNTROPHIN (59 KDA DYSTROPHIN-ASSOCIATED PROTEIN A1, BASIC COMPONENT 2) (SYNTROPHIN 3) (SNT3) (SYNTROPHIN-LIKE) (SNTL). [SWISSPROT;Acc:Q13425]" 0.0666089 SNTB2 0.248059362
1211 0.259184 ANGIOMOTIN LIKE 2; LEMAN COILED-COIL PROTEIN; ANGIOMOTIN-LIKE PROTEIN 2. [RefSeq;Acc:NM_016201] 0.064293 AMOTL2 0.248059294
1212 0.489504 "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 DBT 0.24805926
1213 0.323509 DYSTROPHIN. [SWISSPROT;Acc:P11532] 0.0802494 no value 0.24805925
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 0.250362 UTROPHIN (DYSTROPHIN-RELATED PROTEIN 1) (DRP1) (DRP). [SWISSPROT;Acc:P46939] 0.0621046 UTRN 0.24805921
1218 0.258242 "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 SNTA1 0.248059185
1219 0.171305 0.0424937 WDR55 0.248058726
1220 3.68475 PESCADILLO HOMOLOG 1. [SWISSPROT;Acc:O00541] 0.913889 PES1 0.248019269
1221 0.722847 VISININ-LIKE PROTEIN 3 (VILIP-3) (CALCIUM-BINDING PROTEIN BDR-1) (HLP2) (HIPPOCALCIN-LIKE PROTEIN 1). [SWISSPROT;Acc:P37235] 0.179279 HPCAL1 0.248017907
1222 3.07607 DYSTROBREVIN ALPHA (DYSTROBREVIN-ALPHA). [SWISSPROT;Acc:Q9Y4J8] 0.762918 DTNA 0.248017113
1223 0.273711 DEAD-BOX PROTEIN 4 (VASA HOMOLOG). [SWISSPROT;Acc:Q9NQI0] 0.0678848 DDX4 0.248016338
1224 0.606896 NEURON SPECIFIC CALCIUM-BINDING PROTEIN HIPPOCALCIN (P23K) (CALCIUM- BINDING PROTEIN BDR-2). [SWISSPROT;Acc:P32076] 0.150518 HPCA 0.248012839
1225 0.592229 NEUROCALCIN DELTA. [SWISSPROT;Acc:P29554] 0.14688 NCALD 0.248012171
1226 4.53144 1.12354 KIAA0020 0.247943259
1227 2.90646 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 SMARCC1 0.247906044
1228 1.07305 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN M (HNRNP M). [SWISSPROT;Acc:P52272] 0.266011 HNRPM 0.247901775
1229 1.39492 ARF GTPASE-ACTIVATING PROTEIN GIT2 (G PROTEIN-COUPLED RECEPTOR KINASE- INTERACTOR 2). [SWISSPROT;Acc:Q14161] 0.345758 GIT2 0.247869412
1230 2.74555 0.6803 RRP12 0.247782776
1231 0.102605 DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 31 ISOFORM 1; DEAD/DEXH HELICASE DDX31. [RefSeq;Acc:NM_022779] 0.0254237 DDX31 0.247782272
1232 0.33749 0.0836052 KIAA0859 0.247726451
1233 0.517633 POLYBROMO 1. [RefSeq;Acc:NM_018165] 0.128218 PBRM1 0.247700591
1234 0.526678 POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L2 (SNF2-ALPHA). [SWISSPROT;Acc:P51531] 0.130458 SMARCA2 0.247699733
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 1.09519 POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L1. [SWISSPROT;Acc:P28370] 0.271278 SMARCA1 0.247699486
1237 1.2397 SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN A5; SUCROSE NONFERMENTING-LIKE 5. [RefSeq;Acc:NM_003601] 0.307072 SMARCA5 0.247698637
1238 1.14255 TBP-ASSOCIATED FACTOR 172 (TAF-172) (TAF(II)170). [SWISSPROT;Acc:O14981] 0.283008 BTAF1 0.247698569
1239 1.13458 "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 KCND1 0.247614976
1240 1.24236 "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 KCND3 0.247611803
1241 1.16536 0.288556 C22orf25 0.247611039
1242 0.319234 CYSTATHIONINE GAMMA-LYASE (EC 4.4.1.1) (GAMMA-CYSTATHIONASE). [SWISSPROT;Acc:P32929] 0.0790456 CTH 0.247610217
1243 1.46751 "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 KCND2 0.24760649
1244 0.213145 "SOLUTE CARRIER FAMILY 2, FACILITATED GLUCOSE TRANSPORTER, MEMBER 6 (GLUCOSE TRANSPORTER TYPE 6) (GLUCOSE TRANSPORTER TYPE 9). [SWISSPROT;Acc:Q9UGQ3]" 0.0527752 SLC2A6 0.247602336
1245 0.280228 "SOLUTE CARRIER FAMILY 2, FACILITATED GLUCOSE TRANSPORTER, MEMBER 8 (GLUCOSE TRANSPORTER TYPE 8) (GLUCOSE TRANSPORTER TYPE X1). [SWISSPROT;Acc:Q9NY64]" 0.069385 SLC2A8 0.247601953
1246 0.563754 DNA-DIRECTED RNA POLYMERASE II 16 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB4). [SWISSPROT;Acc:O15514] 0.139566 POLR2D 0.247565427
1247 5.16557 FIBRILLARIN (34 KDA NUCLEOLAR SCLERODERMA ANTIGEN). [SWISSPROT;Acc:P22087] 1.27878 FBL 0.247558353
1248 2.69939 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 SMARCC2 0.247518884
1249 0.476127 60S ACIDIC RIBOSOMAL PROTEIN P0 (L10E). [SWISSPROT;Acc:P05388] 0.11779 RPLP0 0.247391977
1250 0.46643 BLOCK 23. [SPTREMBL;Acc:Q8NHW5] 0.11539 no value 0.247389748

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/