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 [...,...].
Hugo measured Rank Gene description expected final
Results: HTML CSV LaTeX Showing element 3058 to 3107 of 3206 in total
Hugo
measured
Rank
description
expected
final
UGP2 0.203313 1611 UTP--GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE 2 (EC 2.7.7.9) (UDP- GLUCOSE PYROPHOSPHORYLASE 2) (UDPGP 2) (UGPASE 2). [SWISSPROT;Acc:Q16851] 0.847819 0.239807081
UMPS 0.485259 2161 URIDINE 5'-MONOPHOSPHATE SYNTHASE (UMP SYNTHASE) [INCLUDES: OROTATE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.10) (OPRTASE); OROTIDINE 5'- PHOSPHATE DECARBOXYLASE (EC 4.1.1.23) (OMPDECASE)]. [SWISSPROT;Acc:P11172] 2.13541 0.227243948
UNC119 0.183433 1816 UNC-119 PROTEIN HOMOLOG (RETINAL PROTEIN 4) (HRG4). [SWISSPROT;Acc:Q13432] 0.783008 0.234267083
UNC84A 0.240086 222 SAD1/UNC-84 PROTEIN-LIKE 1. [SWISSPROT;Acc:O94901] 0.755227 0.317899122
UNG 0.0946707 1739 "URACIL-DNA GLYCOSYLASE, MITOCHONDRIAL PRECURSOR (EC 3.2.2.-) (UDG). [SWISSPROT;Acc:P13051]" 0.399507 0.236968814
UPRT 0.108852 1297 0.442722 0.245869869
UQCRB 0.0993399 395 UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KDA PROTEIN (EC 1.10.2.2) (COMPLEX III SUBUNIT VI) (QP-C). [SWISSPROT;Acc:P14927] 0.356562 0.278604843
UQCRC1 0.167149 2498 "UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I, MITOCHONDRIAL PRECURSOR (EC 1.10.2.2). [SWISSPROT;Acc:P31930]" 0.776201 0.215342418
UQCRFSL1 0.102272 1905 "UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.10.2.2) (RIESKE IRON-SULFUR PROTEIN) (RISP). [SWISSPROT;Acc:P47985]" 0.440396 0.232227359
URM1 0.0280218 2387 0.127549 0.219694392
USF1 0.0867894 2352 UPSTREAM STIMULATORY FACTOR 1 (MAJOR LATE TRANSCRIPTION FACTOR 1). [SWISSPROT;Acc:P22415] 0.39382 0.220378345
USF2 0.0736246 2354 UPSTREAM STIMULATORY FACTOR 2 (UPSTREAM TRANSCRIPTION FACTOR 2) (FOS-INTERACTING PROTEIN) (FIP) (MAJOR LATE TRANSCRIPTION FACTOR 2). [SWISSPROT;Acc:Q15853] 0.334101 0.220366296
USO1 1.73296 404 GENERAL VESICULAR TRANSPORT FACTOR P115 (TRANSCYTOSIS ASSOCIATED PROTEIN) (TAP) (VESICLE DOCKING PROTEIN). [SWISSPROT;Acc:O60763] 6.22802 0.278252157
USP30 0.167849 670 0.629342 0.266705543
USP47 0.160096 699 0.603029 0.265486403
USP52 0.206722 2381 0.940952 0.219694522
USP8 0.0884444 421 UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 8 (EC 3.1.2.15) (UBIQUITIN THIOLESTERASE 8) (UBIQUITIN-SPECIFIC PROCESSING PROTEASE 8) (DEUBIQUITINATING ENZYME 8). [SWISSPROT;Acc:P40818] 0.318867 0.277370816
UTP14A 0.0771492 908 SEROLOGICALLY DEFINED COLON CANCER ANTIGEN 16. [RefSeq;Acc:NM_006649] 0.298726 0.258260747
UTP15 0.539944 1441 2.21735 0.243508693
UTP18 0.127901 1453 0.525864 0.243220681
UTP20 1.17672 1526 DOWN-REGULATED IN METASTASIS. [RefSeq;Acc:NM_014503] 4.8561 0.242317909
UTP3 0.144805 2710 DISRUPTER OF SILENCING 10. [RefSeq;Acc:NM_020368] 0.698382 0.207343546
UTRN 0.0621046 1217 UTROPHIN (DYSTROPHIN-RELATED PROTEIN 1) (DRP1) (DRP). [SWISSPROT;Acc:P46939] 0.250362 0.24805921
UXT 0.0305539 1788 UXT PROTEIN (UBIQUITOUSLY EXPRESSED TRANSCRIPT PROTEIN) (HSPC024). [SWISSPROT;Acc:Q9UBK9] 0.129981 0.235064356
VAC14 0.311829 1485 1.28408 0.242842346
VAMP1 0.0233268 2734 VESICLE-ASSOCIATED MEMBRANE PROTEIN 1 (VAMP-1) (SYNAPTOBREVIN 1). [SWISSPROT;Acc:P23763] 0.113606 0.205330704
VAMP2 0.0252114 2737 VESICLE-ASSOCIATED MEMBRANE PROTEIN 2 (VAMP-2) (SYNAPTOBREVIN 2). [SWISSPROT;Acc:P19065] 0.122785 0.205329641
VAMP3 0.0215242 2735 VESICLE-ASSOCIATED MEMBRANE PROTEIN 3 (VAMP-3) (SYNAPTOBREVIN 3) (CELLUBREVIN) (CEB). [SWISSPROT;Acc:Q15836] 0.104827 0.205330688
VAMP4 0.0252114 2739 VESICULE-ASSOCIATED MEMBRANE PROTEIN 4 (VAMP-4). [SWISSPROT;Acc:O75379] 0.122785 0.205329641
VARS 0.0546688 1832 VALYL-TRNA SYNTHETASE 2 (EC 6.1.1.9) (VALINE--TRNA LIGASE 2) (VALRS 2) (G7A). [SWISSPROT;Acc:P26640] 0.233559 0.234068479
VAV1 0.379284 98 VAV PROTO-ONCOGENE. [SWISSPROT;Acc:P15498] 1.01082 0.375224076
VAV2 0.433722 105 VAV-2 PROTEIN. [SWISSPROT;Acc:P52735] 1.16696 0.371668266
VAV3 0.380273 99 VAV-3 PROTEIN. [SWISSPROT;Acc:Q9UKW4] 1.015 0.374653202
VBP1 0.0305539 1787 PREFOLDIN SUBUNIT 3 (VON HIPPEL-LINDAU BINDING PROTEIN 1) (VHL BINDING PROTEIN-1) (VBP-1) (HIBBJ46). [SWISSPROT;Acc:Q15765] 0.129981 0.235064356
VCL 0.253265 226 VINCULIN (METAVINCULIN). [SWISSPROT;Acc:P18206] 0.799038 0.316962397
VCP 0.261495 325 TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE (TER ATPASE) (15S MG(2+)- ATPASE P97 SUBUNIT) (VALOSIN CONTAINING PROTEIN) (VCP) [CONTAINS: VALOSIN]. [SWISSPROT;Acc:P55072] 0.912016 0.286721943
VPS11 0.167384 918 VACUOLAR PROTEIN SORTING 11 (HVPS11) (PP3476). [SWISSPROT;Acc:Q9H270] 0.648924 0.257940837
VPS18 0.21331 897 VACUOLAR PROTEIN SORTING 18 (HVPS18). [SWISSPROT;Acc:Q9P253] 0.821874 0.259541
VPS24 0.027115 3197 NEUROENDOCRINE DIFFERENTIATION FACTOR; COMPARATIVE GENE IDENTIFICATION TRANSCRIPT 149. [RefSeq;Acc:NM_016079] 0.735578 0.036862168
VPS25 0.10685 1725 0.450769 0.23703937
VPS29 0.179287 2646 VACUOLAR PROTEIN SORTING 29 (VESICLE PROTEIN SORTING 29) (HVPS29) (MDS007) (PEP11) (DC7/DC15). [SWISSPROT;Acc:Q9UBQ0] 0.8539 0.209962525
VPS33A 0.132652 916 VACUOLAR PROTEIN SORTING 33A (HVPS33A). [SWISSPROT;Acc:Q96AX1] 0.514271 0.257941824
VPS33B 0.104198 917 VACUOLAR PROTEIN SORTING 33B (HVPS33B). [SWISSPROT;Acc:Q9H267] 0.40396 0.25794138
VPS35 0.0319827 2650 VACUOLAR PROTEIN SORTING 35 (VESICLE PROTEIN SORTING 35) (HVPS35) (MATERNAL-EMBRYONIC 3). [SWISSPROT;Acc:Q96QK1] 0.152326 0.209962186
VPS37B 0.107134 2938 0.682084 0.157068631
VPS37C 0.0831672 2936 0.529029 0.157207261
VPS39 0.403209 1896 VAM6/VPS39-LIKE PROTEIN (HVAM6P). [SWISSPROT;Acc:Q96JC1] 1.73336 0.232616998
VPS45 0.230384 1723 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 45 (H-VPS45) (HLVPS45). [SWISSPROT;Acc:Q9NRW7] 0.971531 0.237134996
VPS52 0.281375 971 SUPPRESSOR OF ACTIN MUTATIONS 2-LIKE ISOFORM B; DJ1033B10.5. [RefSeq;Acc:NM_022553] 1.10102 0.255558482
VPS72 0.0253936 2601 YL-1 PROTEIN (TRANSCRIPTION FACTOR-LIKE 1). [SWISSPROT;Acc:Q15906] 0.119307 0.212842499

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/