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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expected Gene Rank measured description final Hugo
Results: HTML CSV LaTeX Showing element 1502 to 1551 of 3206 in total
expected
Rank
measured
description
final
Hugo
0.485577 211 0.155654 GLUTATHIONE TRANSFERASE OMEGA 1 (EC 2.5.1.18) (GSTO 1-1). [SWISSPROT;Acc:P78417] 0.320554721 GSTO1
212 "ATP SYNTHASE B CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P24539]" ATP5F1
213 RD PROTEIN. [SWISSPROT;Acc:P18615] no value
214 J DOMAIN CONTAINING PROTEIN 1. [SWISSPROT;Acc:Q9UKB3] DNAJC12
215 PP3111 PROTEIN. [RefSeq;Acc:NM_022156] DUS1L
0.485769 2394 0.106596 "BLOOM'S SYNDROME PROTEIN (EC 3.6.1.-) (RECQ PROTEIN-LIKE 3) (DNA HELICASE, RECQ-LIKE, TYPE 2). [SWISSPROT;Acc:P54132]" 0.219437634 no value
0.486077 3181 0.0241952 CULLIN HOMOLOG 2 (CUL-2). [SWISSPROT;Acc:Q13617] 0.049776476 CUL2
0.486357 3195 0.0179282 ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM. [RefSeq;Acc:NM_006463] 0.036862223 STAMBP
0.486671 2753 0.099187 0.203807089 PGAM5
0.487324 415 0.135171 SAL-LIKE PROTEIN 4 (ZINC FINGER PROTEIN SALL4). [SWISSPROT;Acc:Q9UJQ4] 0.277373985 SALL4
0.487402 2760 0.0987657 SERINE/THREONINE PROTEIN PHOSPHATASE 6 (EC 3.1.3.16) (PP6). [SWISSPROT;Acc:O00743] 0.202637043 PPP6C
0.487701 8 0.281519 ODD-SKIPPED RELATED 1; ODZ (ODD OZ/TEN-M) RELATED 1. [RefSeq;Acc:NM_145260] 0.577236873 OSR1
0.488304 45 0.203633 GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE PROTEIN GADD45 GAMMA (CYTOKINE RESPONSIVE PROTEIN CR6). [SWISSPROT;Acc:O95257] 0.417020954 GADD45G
0.489392 832 0.127743 ITCHY HOMOLOG E3 UBIQUITIN PROTEIN LIGASE; ATROPHIN-1 INTERACTING PROTEIN 4; ITCHY (MOUSE HOMOLOG) E3 UBIQUITIN PROTEIN LIGASE; NFE2-ASSOCIATED POLYPEPTIDE 1; UBIQUITIN PROTEIN LIGASE ITCH. [RefSeq;Acc:NM_031483] 0.261023883 ITCH
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]" 0.24805926 DBT
0.490121 1252 0.121247 METHYLENETETRAHYDROFOLATE REDUCTASE (EC 1.5.1.20). [SWISSPROT;Acc:P42898] 0.247381769 MTHFR
0.490411 2343 0.108234 MEIOTIC RECOMBINATION PROTEIN DMC1/LIM15 HOMOLOG. [SWISSPROT;Acc:Q14565] 0.220700596 DMC1
0.490424 598 0.132014 CAMP RESPONSE ELEMENT-BINDING PROTEIN CRE-BPA. [RefSeq;Acc:NM_004904] 0.2691834 CREB5
0.490447 2023 0.112993 "MAGUK P55 SUBFAMILY MEMBER 3 (MPP3 PROTEIN) (DISCS, LARGE HOMOLOG 3). [SWISSPROT;Acc:Q13368]" 0.230387789 MPP3
0.491473 1572 0.11844 MITOCHONDRIAL PRECURSOR PROTEINS IMPORT RECEPTOR (TRANSLOCASE OF OUTER MEMBRANE TOM70). [SWISSPROT;Acc:O94826] 0.240989841 TOMM70A
0.49236 360 0.138286 EXOCYST COMPLEX COMPONENT SEC15A. [SWISSPROT;Acc:Q8TAG9] 0.280863596 EXOC6
0.493083 508 0.135095 HEAT SHOCK FACTOR BINDING PROTEIN 1. [SWISSPROT;Acc:O75506] 0.273980243 no value
0.493701 2720 0.10212 0.206845844 MCTP1
0.494121 267 0.152054 0.307726245 no value
0.494224 793 0.129493 "BETA-SOLUBLE NSF ATTACHMENT PROTEIN (SNAP-BETA) (N-ETHYLMALEIMIDE- SENSITIVE FACTOR ATTACHMENT PROTEIN, BETA). [SWISSPROT;Acc:Q9H115]" 0.262012772 NAPB
0.494524 96 0.185899 POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 1 (POTASSIUM CHANNEL KV1.1) (HUKI) (HBK1). [SWISSPROT;Acc:Q09470] 0.375915021 KCNA1
0.494891 902 0.128336 LIMBIC SYSTEM-ASSOCIATED MEMBRANE PROTEIN PRECURSOR (LSAMP). [SWISSPROT;Acc:Q13449] 0.25932175 LSAMP
0.494902 1659 0.118202 TCD37 HOMOLOG; PRUNE. [RefSeq;Acc:NM_021222] 0.238839205 PRUNE
0.495798 1275 0.122196 PROTEASOME SUBUNIT BETA TYPE 9 PRECURSOR (EC 3.4.25.1) (PROTEASOME CHAIN 7) (MACROPAIN CHAIN 7) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX CHAIN 7) (RING12 PROTEIN) (LOW MOLECULAR MASS PROTEIN 2). [SWISSPROT;Acc:P28065] 0.246463277 no value
0.495862 1012 0.126011 BETA-CATENIN (PRO2286). [SWISSPROT;Acc:P35222] 0.25412514 CTNNB1
0.496001 965 0.12694 CHROMATIN-SPECIFIC TRANSCRIPTION ELONGATION FACTOR LARGE SUBUNIT. [RefSeq;Acc:NM_007192] 0.255926903 SUPT16H
0.497084 2200 0.11223 CYTOCHROME B5 REDUCTASE 1 (B5R.1). [RefSeq;Acc:NM_016243] 0.22577673 CYB5R1
0.497941 2953 0.0735334 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 56 KDA REGULATORY SUBUNIT, EPSILON ISOFORM (PP2A, B SUBUNIT, B' EPSILON ISOFORM) (PP2A, B SUBUNIT, B56 EPSILON ISOFORM) (PP2A, B SUBUNIT, PR61 EPSILON ISOFORM) (PP2A, B SUBUNIT, R5 EPSILON ISOFORM). [SWISSPR" 0.147674925 PPP2R5E
0.497956 2199 0.112427 CYTOCHROME B5 REDUCTASE B5R.2. [RefSeq;Acc:NM_016229] 0.225776976 CYB5R2
0.498014 3089 0.048624 0.097635809 TM4SF19
3090 METHYLTRANSFERASE LIKE 2. [RefSeq;Acc:NM_018396] no value
3091 METTL2A
3092 FZR1 PROTEIN; FIZZY-RELATED PROTEIN; CDC20-LIKE 1B. [RefSeq;Acc:NM_016263] FZR1
0.499271 2031 0.114962 PROTEIN TRANSPORT PROTEIN SEC61 GAMMA SUBUNIT. [SWISSPROT;Acc:P38384] 0.230259719 SEC61G
0.5 10 0.271296 PROTEIN X 0004. [RefSeq;Acc:NM_016301] 0.542592 ATPBD1C
12 0.250879 HBS1-LIKE. [RefSeq;Acc:NM_006620] 0.501758 HBS1L
13 HOMEOBOX PROTEIN HLX1 (HOMEOBOX PROTEIN HB24). [SWISSPROT;Acc:Q14774] HLX
24 0.229891 0.459782 CNOT10
0.501115 150 0.176025 "KH DOMAIN CONTAINING, RNA BINDING, SIGNAL TRANSDUCTION ASSOCIATED 1; GAP-ASSOCIATED TYROSINE PHOSPHOPROTEIN P62 (SAM68). [RefSeq;Acc:NM_006559]" 0.351266675 KHDRBS1
0.50235 1276 0.123807 "MAGUK P55 SUBFAMILY MEMBER 2 (MPP2 PROTEIN) (DISCS, LARGE HOMOLOG 2). [SWISSPROT;Acc:Q14168]" 0.246455658 MPP2
0.502445 2446 0.109079 LARGE PROLINE-RICH PROTEIN BAT3 (HLA-B-ASSOCIATED TRANSCRIPT 3) (G3). [SWISSPROT;Acc:P46379] 0.217096399 no value
0.504182 427 0.139845 GROWTH-ARREST-SPECIFIC PROTEIN 7 (GAS-7). [SWISSPROT;Acc:O60861] 0.277370077 GAS7
0.504282 388 0.140567 "SWI/SNF RELATED, MATRIX ASSOCIATED, ACTIN DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY D MEMBER 1 (SWI/SNF COMPLEX 60 KDA SUBUNIT) (BRG1- ASSOCIATED FACTOR 60A). [SWISSPROT;Acc:Q96GM5]" 0.278746812 SMARCD1
0.504416 894 0.131086 KINESIN HEAVY CHAIN (UBIQUITOUS KINESIN HEAVY CHAIN) (UKHC). [SWISSPROT;Acc:P33176] 0.259876768 KIF5B
0.504447 1261 0.12467 0.24714192 no value

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/