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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 2808 to 2857 of 3206 in total
Rank
description
measured
expected
final
Hugo
2808 PEROXISOMAL TARGETING SIGNAL 2 RECEPTOR (PTS2 RECEPTOR) (PEROXIN-7). [SWISSPROT;Acc:O00628] 0.141529 0.715904 0.197692707 PEX7
2809 0.124033 0.627474 0.197670342 ZBTB45
2810 TUMOR PROTEIN D54 (HD54) (D52-LIKE 2). [SWISSPROT;Acc:O43399] 0.149456 0.75755 0.197288628 TPD52L2
2811 0.0949008 0.481532 0.197080983 RPP25
2812 0.121488 0.616542 0.197047403 C9orf23
2813 UBIQUITIN-SPECIFIC PROTEASE OTUBAIN 1. [RefSeq;Acc:NM_017670] 0.189314 0.96599 0.195979254 OTUB1
2814 "ACYL-COA DEHYDROGENASE, VERY-LONG-CHAIN SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 1.3.99.-) (VLCAD). [SWISSPROT;Acc:P49748]" 0.0780112 0.399468 0.195287733 ACADVL
2815 SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT-CONTAINING PROTEIN (VPU-BINDING PROTEIN) (UBP). [SWISSPROT;Acc:O43765] 0.897082 4.61021 0.19458593 SGTA
2816 ZINC FINGER PROTEIN 444; ENDOTHELIAL ZINC FINGER PROTEIN 2. [RefSeq;Acc:NM_018337] 0.225841 1.1643 0.193971485 ZNF444
2817 ZINC FINGER PROTEIN 274 (ZINC FINGER PROTEIN SP2114) (ZINC FINGER PROTEIN HFB101) (ZINC FINGER PROTEIN ZFP2) (ZF2). [SWISSPROT;Acc:Q96GC6] 0.166977 0.862746 0.19354132 ZNF274
2818 ZINC FINGER PROTEIN 213 (PUTATIVE TRANSCRIPTION FACTOR CR53). [SWISSPROT;Acc:O14771] 0.166266 0.8591 0.193535095 ZNF213
2819 ZINC FINGER PROTEIN 99. [RefSeq;Acc:NM_032164] 0.166195 0.858735 0.193534676 ZNF394
2820 ZINC FINGER PROTEIN 232. [SWISSPROT;Acc:Q9UNY5] 0.16591 0.857277 0.193531379 ZNF232
2821 ZINC FINGER PROTEIN 305. [SWISSPROT;Acc:O43309] 0.165839 0.856912 0.193530958 ZSCAN12
2822 0.164985 0.852537 0.193522393 ZNF449
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 0.851807 0.193520363 ZNF24
2824 0.164486 0.849984 0.193516584 ZNF496
2825 ZINC FINGER PROTEIN 215 (BWSCR2 ASSOCIATED ZINC-FINGER PROTEIN 2) (BAZ 2). [SWISSPROT;Acc:Q9UL58] ZNF215
2826 ZINC FINGER PROTEIN 18 (ZINC FINGER PROTEIN KOX11) (FRAGMENT). [SWISSPROT;Acc:P17022] 0.164415 0.84962 0.193515925 ZNF18
2827 ZINC FINGER IMPRINTED 2. [SWISSPROT;Acc:Q9NZV7] 0.161283 0.833576 0.193483258 no value
2828 ZINC FINGER PROTEIN 174 (AW-1). [SWISSPROT;Acc:Q15697] 0.158934 0.821543 0.19345792 ZNF174
2829 DOLICHOL-PHOSPHATE MANNOSYLTRANSFERASE (EC 2.4.1.83) (DOLICHOL- PHOSPHATE MANNOSE SYNTHASE) (DOLICHYL-PHOSPHATE BETA-D- MANNOSYLTRANSFERASE) (MANNOSE-P-DOLICHOL SYNTHASE) (MPD SYNTHASE) (DPM SYNTHASE). [SWISSPROT;Acc:O60762] 0.349731 1.80836 0.193396779 DPM1
2830 TETRANECTIN PRECURSOR (TN) (PLASMINOGEN-KRINGLE 4 BINDING PROTEIN). [SWISSPROT;Acc:P05452] 0.259669 1.34352 0.193275128 CLEC3B
2831 CALSYNTENIN-3 PRECURSOR. [SWISSPROT;Acc:Q9BQT9] 0.0641829 0.33238 0.193100969 CLSTN3
2832 CALSYNTENIN-2 PRECURSOR. [SWISSPROT;Acc:Q9H4D0] 0.0653044 0.338193 0.193098024 CLSTN2
2833 PROTEIN-TYROSINE PHOSPHATASE BETA PRECURSOR (EC 3.1.3.48) (R-PTP- BETA). [SWISSPROT;Acc:P23467] 0.036734 0.190263 0.193069593 PTPRB
2834 GK001 PROTEIN. [RefSeq;Acc:NM_020198] 0.157265 0.814552 0.193069319 CCDC47
2835 "SUCCINATE DEHYDROGENASE [UBIQUINONE] CYTOCHROME B SMALL SUBUNIT, MITOCHONDRIAL PRECURSOR (CYBS) (SUCCINATE-UBIQUINONE REDUCTASE MEMBRANE ANCHOR SUBUNIT) (QPS2) (CII-4) (SUCCINATE DEHYDROGENASE COMPLEX SUBUNIT D) (SUCCINATE-UBIQUINONE OXIDOREDUCTASE CYTOCH" 0.0431276 0.223379 0.193069178 no value
2836 CALSYNTENIN-1 PRECURSOR. [SWISSPROT;Acc:O94985] 0.0775327 0.40158 0.193069127 CLSTN1
2837 THYMUS-SPECIFIC SERINE PROTEASE PRECURSOR (EC 3.4.-.-). [SWISSPROT;Acc:Q9NQE7] 0.0430845 0.223156 0.193068974 PRSS16
2838 "TRANSLOCON-ASSOCIATED PROTEIN, DELTA SUBUNIT PRECURSOR (TRAP-DELTA) (SIGNAL SEQUENCE RECEPTOR DELTA SUBUNIT) (SSR-DELTA). [SWISSPROT;Acc:P51571]" 0.12066 0.62496 0.193068356 SSR4
2839 AQUAPORIN-CHIP (WATER CHANNEL PROTEIN FOR RED BLOOD CELLS AND KIDNEY PROXIMAL TUBULE) (AQUAPORIN 1) (AQP-1) (URINE WATER CHANNEL). [SWISSPROT;Acc:P29972] 0.0800859 0.415411 0.192787143 AQP1
2840 LENS FIBER MAJOR INTRINSIC PROTEIN (MIP26) (MP26) (AQUAPORIN 0). [SWISSPROT;Acc:P30301] 0.0610425 0.316697 0.192747326 MIP
2841 AQUAPORIN-CD (AQP-CD) (WATER CHANNEL PROTEIN FOR RENAL COLLECTING DUCT) (ADH WATER CHANNEL) (AQUAPORIN 2) (COLLECTING DUCT WATER CHANNEL PROTEIN) (WCH-CD). [SWISSPROT;Acc:P41181] 0.0608484 0.315691 0.192746705 AQP2
2842 AQUAPORIN 5. [SWISSPROT;Acc:P55064] 0.0604602 0.313678 0.192746064 AQP5
2843 AQUAPORIN 4 (WCH4) (MERCURIAL-INSENSITIVE WATER CHANNEL) (MIWC). [SWISSPROT;Acc:P55087] 0.0599642 0.311107 0.192744618 AQP4
2844 C-TYPE LECTIN SUPERFAMILY MEMBER 1 PRECURSOR (CARTILAGE-DERIVED C-TYPE LECTIN). [SWISSPROT;Acc:O75596] 0.188839 0.981321 0.192433465 CLEC3A
2845 STEM CELL GROWTH FACTOR; LYMPHOCYTE SECRETED C-TYPE LECTIN; LYMPHOCYTE SECRETED C-TYPE LECTIN. [RefSeq;Acc:NM_002975] 0.164601 0.857382 0.191980937 CLEC11A
2846 "RED CELL ACID PHOSPHATASE 1, ISOZYME F (EC 3.1.3.2) (ACP1) (LOW MOLECULAR WEIGHT PHOSPHOTYROSINE PROTEIN PHOSPHATASE) (EC 3.1.3.48) (ADIPOCYTE ACID PHOSPHATASE, ISOZYME ALPHA). [SWISSPROT;Acc:P24666]" 0.0987604 0.514942 0.191789367 ACP1
2847 JUNCTOPHILIN 2 (JUNCTOPHILIN TYPE 2) (JP-2). [SWISSPROT;Acc:Q9BR39] 0.156536 0.818 0.191364303 JPH2
2848 JUNCTOPHILIN 3 (JUNCTOPHILIN TYPE 3) (JP-3). [SWISSPROT;Acc:Q8WXH2] 0.156823 0.8195 0.191364246 JPH3
2849 SPHINGOMYELIN PHOSPHODIESTERASE 2 (EC 3.1.4.12) (NEUTRAL SPHINGOMYELINASE) (NSMASE) (N-SMASE) (LYSO-PLATELET ACTIVATING FACTOR- PHOSPHOLIPASE C) (LYSO-PAF-PLC). [SWISSPROT;Acc:O60906] 0.696087 3.6375 0.191364124 SMPD2
2850 DB83 PROTEIN. [SWISSPROT;Acc:P57088] 0.191364 1 0.191364 TMEM33
2851 "PROTEIN PHOSPHATASE 1, REGULATORY SUBUNIT 7; SDS22. [RefSeq;Acc:NM_002712]" 0.0699506 0.365592 0.19133515 PPP1R7
2852 SMALL GLUTAMINE RICH PROTEIN WITH TETRATRICOPEPTIDE REPEATS 2. [RefSeq;Acc:NM_019072] 0.839834 4.39067 0.191276958 no value
2853 "ISOCITRATE DEHYDROGENASE [NADP], MITOCHONDRIAL PRECURSOR (EC 1.1.1.42) (OXALOSUCCINATE DECARBOXYLASE) (IDH) (NADP+-SPECIFIC ICDH) (IDP) (ICD-M). [SWISSPROT;Acc:P48735]" 0.0716408 0.374722 0.191183864 IDH2
2854 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE DELTA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 4) (1-AGPAT 4) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-DELTA) (LPAAT-DELTA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 4). [SWISSPROT;Acc:Q9NRZ5] 0.24139 1.26323 0.191089509 AGPAT4
2855 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE GAMMA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 3) (1-AGPAT 3) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-GAMMA) (LPAAT-GAMMA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 3). [SWISSPROT;Acc:Q9NRZ7] 0.214138 1.12158 0.190925302 AGPAT3
2856 TRIOSEPHOSPHATE ISOMERASE (EC 5.3.1.1) (TIM). [SWISSPROT;Acc:P00938] 0.158456 0.830447 0.190808083 TPI1
2857 TRNA (5-METHYLAMINOMETHYL-2-THIOURIDYLATE)-METHYLTRANSFERASE (EC 2.1.1.61). [SWISSPROT;Acc:O75648] 0.0583389 0.30593 0.190693623 TRMU

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/