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 description measured final Hugo
Results: HTML CSV LaTeX Showing element 2102 to 2151 of 3206 in total
expected
Rank
description
measured
final
Hugo
0.846512 3173 NUCLEAR RNA EXPORT FACTOR 3 (TAP-LIKE PROTEIN 3) (TAPL-3). [SWISSPROT;Acc:Q9H4D5] 0.0469672 0.055483206 NXF3
0.846836 2283 0.188344 0.222409061 GDPD1
0.847008 1676 "54 KDA NUCLEAR RNA- AND DNA-BINDING PROTEIN (P54(NRB)) (P54NRB) (55 KDA NUCLEAR PROTEIN) (NMT55) (NON-POU DOMAIN-CONTAINING OCTAMER- BINDING PROTEIN) (DNA-BINDING P52/P100 COMPLEX, 52 KDA SUBUNIT). [SWISSPROT;Acc:Q15233]" 0.201833 0.238289367 NONO
0.847287 2110 "ZINC RIBBON DOMAIN CONTAINING, 1; TRANSCRIPTION-ASSOCIATED ZINC RIBBON PROTEIN; RNA POLYMERASE I SMALL SPECIFIC SUBUNIT RPA12. [RefSeq;Acc:NM_014596]" 0.193407 0.228266219 ZNRD1
0.847805 2706 "STEROID HORMONE RECEPTOR ERR2 (ESTROGEN-RELATED RECEPTOR, BETA) (ERR-BETA) (ESTROGEN RECEPTOR-LIKE 2) (ERR BETA-2). [SWISSPROT;Acc:O95718]" 0.175846 0.207413261 ESRRB
0.847819 1611 UTP--GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE 2 (EC 2.7.7.9) (UDP- GLUCOSE PYROPHOSPHORYLASE 2) (UDPGP 2) (UGPASE 2). [SWISSPROT;Acc:Q16851] 0.203313 0.239807081 UGP2
0.848743 1883 "CREATINE KINASE, SARCOMERIC MITOCHONDRIAL PRECURSOR (EC 2.7.3.2) (S- MTCK) (MIB-CK) (BASIC-TYPE MITOCHONDRIAL CREATINE KINASE). [SWISSPROT;Acc:P17540]" 0.197547 0.232752435 CKMT2
0.84962 2826 ZINC FINGER PROTEIN 18 (ZINC FINGER PROTEIN KOX11) (FRAGMENT). [SWISSPROT;Acc:P17022] 0.164415 0.193515925 ZNF18
0.849984 2824 0.164486 0.193516584 ZNF496
2825 ZINC FINGER PROTEIN 215 (BWSCR2 ASSOCIATED ZINC-FINGER PROTEIN 2) (BAZ 2). [SWISSPROT;Acc:Q9UL58] ZNF215
0.850269 2892 UBIQUITIN ACTIVATING ENZYME E1-LIKE PROTEIN. [RefSeq;Acc:NM_006395] 0.151451 0.178121277 no value
0.850576 563 0.230346 0.270811779 BTBD9
0.850955 2967 RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR (RALGEF) (RALGDS). [SWISSPROT;Acc:Q12967] 0.122631 0.144109853 RALGDS
0.851392 310 NUCLEAR PORE COMPLEX PROTEIN NUP88 (NUCLEOPORIN NUP88) (88 KDA NUCLEAR PORE COMPLEX PROTEIN). [SWISSPROT;Acc:Q99567] 0.251667 0.295594744 NUP88
0.851807 2823 ZINC FINGER PROTEIN 24 (ZINC FINGER PROTEIN 191) (ZINC FINGER PROTEIN KOX17) (RETINOIC ACID SUPPRESSION PROTEIN A) (RSG-A). [SWISSPROT;Acc:P17028] 0.164842 0.193520363 ZNF24
0.852079 1719 VACUOLAR PROTON TRANSLOCATING ATPASE 116 KDA SUBUNIT A ISOFORM 3 (V- ATPASE 116-KDA ISOFORM A3) (OSTEOCLASTIC PROTON PUMP 116 KDA SUBUNIT) (OC-116 KDA) (OC116) (T-CELL IMMUNE REGULATOR 1) (T CELL IMMUNE RESPONSE CDNA7 PROTEIN) (TIRC7). [SWISSPROT;A 0.202198 0.237299593 TCIRG1
0.852537 2822 0.164985 0.193522393 ZNF449
0.853273 576 PEROXISOMAL ACYL-COENZYME A THIOESTER HYDROLASE 2A (EC 3.1.2.2) (PEROXISOMAL LONG-CHAIN ACYL-COA THIOESTERASE 2) (ZAP128). [SWISSPROT;Acc:P49753] 0.230682 0.270349583 ACOT1
0.853344 2802 TUMOR PROTEIN D52 (N8 PROTEIN). [SWISSPROT;Acc:P55327] 0.169565 0.198706501 TPD52
0.853372 3189 MICROFIBRIL-ASSOCIATED GLYCOPROTEIN 4 PRECURSOR. [SWISSPROT;Acc:P55083] 0.0318436 0.037315028 MFAP4
0.853581 1675 PARASPECKLE PROTEIN 1. [RefSeq;Acc:NM_018282] 0.203402 0.238292558 PSPC1
0.853699 25 DNA-REPAIR PROTEIN COMPLEMENTING XP-G CELLS (XERODERMA PIGMENTOSUM GROUP G COMPLEMENTING PROTEIN) (DNA EXCISION REPAIR PROTEIN ERCC-5). [SWISSPROT;Acc:P28715] 0.364125 0.426526211 ERCC5
0.8539 2646 VACUOLAR PROTEIN SORTING 29 (VESICLE PROTEIN SORTING 29) (HVPS29) (MDS007) (PEP11) (DC7/DC15). [SWISSPROT;Acc:Q9UBQ0] 0.179287 0.209962525 VPS29
0.854644 1026 SHORT TRANSIENT RECEPTOR POTENTIAL CHANNEL 5 (TRPC5) (HTRP-5) (HTRP5). [SWISSPROT;Acc:Q9UL62] 0.2166 0.253438859 TRPC5
1027 EBP50-PDZ INTERACTOR OF 64 KDA (EPI64 PROTEIN). [SWISSPROT;Acc:Q9BXI6] TBC1D10A
0.85608 3196 0.031557 0.036862209 CHMP4B
0.856628 533 SMALL NUCLEAR RIBONUCLEOPROTEIN F (SNRNP-F) (SM PROTEIN F) (SM-F) (SMF). [SWISSPROT;Acc:Q15356] 0.232461 0.271367501 SNRPF
0.856912 2821 ZINC FINGER PROTEIN 305. [SWISSPROT;Acc:O43309] 0.165839 0.193530958 ZSCAN12
0.856983 1882 "CREATINE KINASE, UBIQUITOUS MITOCHONDRIAL PRECURSOR (EC 2.7.3.2) (U- MTCK) (MIA-CK) (ACIDIC-TYPE MITOCHONDRIAL CREATINE KINASE). [SWISSPROT;Acc:P12532]" 0.199469 0.232757243 no value
0.857277 2820 ZINC FINGER PROTEIN 232. [SWISSPROT;Acc:Q9UNY5] 0.16591 0.193531379 ZNF232
0.857352 3052 "BASIC HELIX-LOOP-HELIX DOMAIN CONTAINING, CLASS B, 5; TRINUCLEOTIDE REPEAT CONTAINING 20. [RefSeq;Acc:NM_152414]" 0.090943 0.106074285 BHLHB5
0.857382 2845 STEM CELL GROWTH FACTOR; LYMPHOCYTE SECRETED C-TYPE LECTIN; LYMPHOCYTE SECRETED C-TYPE LECTIN. [RefSeq;Acc:NM_002975] 0.164601 0.191980937 CLEC11A
0.858735 2819 ZINC FINGER PROTEIN 99. [RefSeq;Acc:NM_032164] 0.166195 0.193534676 ZNF394
0.8591 2818 ZINC FINGER PROTEIN 213 (PUTATIVE TRANSCRIPTION FACTOR CR53). [SWISSPROT;Acc:O14771] 0.166266 0.193535095 ZNF213
0.860216 161 PREIMPLANTATION PROTEIN 3; LIKELY ORTHOLOG OF PREIMPLANTATION PROTEIN 3. [RefSeq;Acc:NM_015387] 0.297365 0.345686432 MOBKL3
0.860412 2884 "DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE, MITOCHONDRIAL PRECURSOR (EC 3.6.1.23) (DUTPASE) (DUTP PYROPHOSPHATASE). [SWISSPROT;Acc:P33316]" 0.158579 0.184305891 DUT
0.862726 498 0.236585 0.274229593 no value
0.862746 2817 ZINC FINGER PROTEIN 274 (ZINC FINGER PROTEIN SP2114) (ZINC FINGER PROTEIN HFB101) (ZINC FINGER PROTEIN ZFP2) (ZF2). [SWISSPROT;Acc:Q96GC6] 0.166977 0.19354132 ZNF274
0.863762 853 CHROMOSOME 11 OPEN READING FRAME2; CHROMOSOME 11 OPEN READING FRAME2. [RefSeq;Acc:NM_013265] 0.22504 0.260534731 C11orf2
0.865296 618 "SERINE/THREONINE PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT, BETA ISOFORM (EC 3.1.3.16) (CALMODULIN-DEPENDENT CALCINEURIN A SUBUNIT, BETA ISOFORM) (CAM-PRP CATALYTIC SUBUNIT). [SWISSPROT;Acc:P16299]" 0.232385 0.268561278 PPP3CB
0.867932 1331 NNP-1 PROTEIN (NOVEL NUCLEAR PROTEIN 1) (NUCLEOLAR PROTEIN NOP52) (NOP52) (D21S2056E). [SWISSPROT;Acc:P56182] 0.213008 0.245420148 RRP1
0.87318 145 SIMILAR TO EXPRESSED SEQUENCE AA415817. [SPTREMBL;Acc:Q8N4Q9] 0.306813 0.351374287 PDXDC1
0.87407 1010 PUTATATIVE 28 KDA PROTEIN. [RefSeq;Acc:NM_020143] 0.222495 0.254550551 PNO1
0.874459 3123 NUCLEAR DNA-BINDING PROTEIN; SMALL UNIQUE NUCLEAR RECEPTOR COREPRESSOR; C1D DNA-BINDING PROTEIN. [RefSeq;Acc:NM_006333] 0.0678638 0.077606612 no value
0.875357 2305 GLUTAMATE CARBOXYPEPTIDASE-LIKE PROTEIN 2 PRECURSOR. [SWISSPROT;Acc:Q96KN2] 0.194519 0.222216764 CNDP1
0.875383 776 TARGET OF MYB PROTEIN 1. [SWISSPROT;Acc:O60784] 0.230424 0.263226496 TOM1
0.876663 2229 AUTOPHAGY PROTEIN 12-LIKE (APG12-LIKE). [SWISSPROT;Acc:O94817] 0.196655 0.224322231 ATG12
0.877587 1471 TRANSCRIPTION FACTOR-LIKE PROTEIN MRGX (MORF-RELATED GENE X PROTEIN) (MORTALITY FACTOR 4-LIKE 2) (MSL3-2 PROTEIN). [SWISSPROT;Acc:Q15014] 0.213242 0.242986735 MORF4L2
0.87768 208 ANDROGEN-INDUCED 1; CGI-103 PROTEIN; ANDROGEN INDUCED PROTEIN. [RefSeq;Acc:NM_016108] 0.281345 0.320555328 AIG1
0.877854 1596 LAMIN B1. [SWISSPROT;Acc:P20700] 0.210907 0.240252935 LMNB1

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/