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 1202 to 1251 of 3206 in total
Rank
description
measured
expected
final
Hugo
1202 0.0689331 0.277567 0.248347606 TMTC4
1203 0.0900162 0.362464 0.248345215 FAM40B
1204 KV CHANNEL INTERACTING PROTEIN 1; VESICLE APC-BINDING PROTEIN; A-TYPE POTASSIUM CHANNEL MODULATORY PROTEIN 1. [RefSeq;Acc:NM_014592] 0.287166 1.15632 0.248344749 KCNIP1
1205 ZINC FINGER PROTEIN T86. [SWISSPROT;Acc:O00488] 0.130571 0.525788 0.248333929 ZNF593
1206 LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS). [SWISSPROT;Acc:Q15046] 0.318597 1.28364 0.248198093 KARS
1207 0.110079 0.443579 0.248160981 no value
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

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/