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 [...,...].
expected Rank Gene measured description Hugo final
Results: HTML CSV LaTeX Showing element 1252 to 1301 of 3206 in total
expected
Rank
measured
description
Hugo
final
0.386406 1370 0.0946163 HISTONE H2B.S (H2B/S). [SWISSPROT;Acc:P57053] no value 0.244862399
0.386626 1024 0.0979873 UBIQUITIN-LIKE PROTEIN SMT3B (SENTRIN 2) (HSMT3). [SWISSPROT;Acc:P55855] 0.253442086
0.387009 2700 0.0804074 HNRPLL 0.207766228
0.387696 2952 0.057253 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 56 KDA REGULATORY SUBUNIT, ALPHA ISOFORM (PP2A, B SUBUNIT, B' ALPHA ISOFORM) (PP2A, B SUBUNIT, B56 ALPHA ISOFORM) (PP2A, B SUBUNIT, PR61 ALPHA ISOFORM) (PP2A, B SUBUNIT, R5 ALPHA ISOFORM). [SWISSPROT;Acc:Q15" PPP2R5A 0.147674982
0.387764 3192 0.0142939 ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM (AMSH) LIKE PROTEIN. [RefSeq;Acc:NM_020799] STAMBPL1 0.03686237
0.387916 2510 0.0833117 AMINOADIPATE-SEMIALDEHYDE SYNTHASE; LYSINE-KETOGLUTARATE REDUCTASE /SACCHAROPINE DEHYDROGENASE; LYSINE-2-OXOGLUTARATE REDUCTASE; AMINOADIPIC SEMIALDEHYDE SYNTHASE. [RefSeq;Acc:NM_005763] AASS 0.214767372
0.388558 1455 0.0944765 "CALCIUM-TRANSPORTING ATPASE TYPE 2C, MEMBER 1 (EC 3.6.3.8) (ATPASE 2C1) (ATP-DEPENDENT CA(2+) PUMP PMR1) (HUSSY-28). [SWISSPROT;Acc:P98194]" ATP2C1 0.243146454
0.389182 488 0.106754 ADP-RIBOSYLATION FACTOR 4. [SWISSPROT;Acc:P18085] ARF4 0.274303539
0.389336 2037 0.0896146 CASEIN KINASE I ALPHA S-LIKE. [RefSeq;Acc:NM_145203] CSNK1A1L 0.23017291
0.389405 2255 0.0868591 STEROL REGULATORY ELEMENT BINDING PROTEIN CLEAVAGE-ACTIVATING PROTEIN (SREBP CLEAVAGE-ACTIVATING PROTEIN) (SCAP). [SWISSPROT;Acc:Q12770] SCAP 0.223055944
2257 0.086859 no value 0.223055688
0.38998 1838 0.0910964 MTHFD1L 0.233592492
0.390211 1797 0.09162 DNA TOPOISOMERASE III ALPHA (EC 5.99.1.2). [SWISSPROT;Acc:Q13472] TOP3A 0.234796046
0.390223 537 0.105783 BROMODOMAIN-CONTAINING PROTEIN 2 (RING3 PROTEIN) (O27.1.1). [SWISSPROT;Acc:P25440] BRD2 0.271083457
0.390892 1365 0.0957148 HISTONE H2B.D (H2B/D). [SWISSPROT;Acc:Q99877] no value 0.24486252
0.391317 667 0.104453 SQV-7-LIKE PROTEIN (FRAGMENT). [SPTREMBL;Acc:O95454] SLC35D2 0.266926814
0.392026 2150 0.0891166 LIFEGUARD; KIAA0950 PROTEIN. [RefSeq;Acc:NM_012306] FAIM2 0.227323188
0.392062 69 0.159227 SYNAPSIN II. [SWISSPROT;Acc:Q92777] SYN2 0.406127092
0.392103 207 0.125691 SYNTAXIN 18. [SWISSPROT;Acc:Q9P2W9] STX18 0.320556078
0.392353 1369 0.0960725 HISTONE H2B.Q (H2B/Q) (H2B-GL105). [SWISSPROT;Acc:Q16778] HIST2H2BA 0.244862407
0.392545 2402 0.0859883 WILLIAMS BEUREN SYNDROME CHROMOSOME REGION 20C ISOFORM 1. [RefSeq;Acc:NM_032158] NSUN5B 0.219053357
0.392576 3001 0.0506272 GABA-A RECEPTOR-ASSOCIATED PROTEIN. [SPTREMBL;Acc:Q9BY60] no value 0.128961526
0.392702 1574 0.0946162 "MICROTUBULE-ACTIN CROSSLINKING FACTOR 1, ISOFORM 4. [SWISSPROT;Acc:Q96PK2]" MACF1 0.240936384
0.39329 967 0.100509 EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1 (ERF1) (EUKARYOTIC RELEASE FACTOR 1) (TB3-1) (C11 PROTEIN). [SWISSPROT;Acc:P46055] ETF1 0.255559511
0.393799 2868 0.0744045 60S RIBOSOMAL PROTEIN L8. [SWISSPROT;Acc:P25120] RPL8 0.188940297
0.39382 2352 0.0867894 UPSTREAM STIMULATORY FACTOR 1 (MAJOR LATE TRANSCRIPTION FACTOR 1). [SWISSPROT;Acc:P22415] USF1 0.220378345
0.394979 673 0.105333 SFT2D3 0.266680001
0.395071 2038 0.0909346 "CASEIN KINASE I, ALPHA ISOFORM (EC 2.7.1.-) (CKI-ALPHA) (CK1). [SWISSPROT;Acc:P48729]" CSNK1A1 0.230172804
0.395349 447 0.109365 REGUCALCIN GENE PROMOTOR REGION RELATED PROTEIN; RGPR-P117. [RefSeq;Acc:NM_033127] SEC16B 0.276629004
0.39545 2786 0.0790566 PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN (EC 6.1.1.20) (PHENYLALANINE- -TRNA LIGASE ALPHA CHAIN) (PHERS) (CML33). [SWISSPROT;Acc:Q9Y285] FARSA 0.199915539
2787 PHENYLALANINE-TRNA SYNTHETASE. [RefSeq;Acc:NM_006567] FARS2
0.396725 89 0.152828 no value 0.385224022
90 SHROOM-RELATED PROTEIN; F-ACTIN-BINDING PROTEIN; LIKELY ORTHOLOG OF MOUSE SHROOM. [RefSeq;Acc:NM_020859] SHROOM3
91 SHROOM4
0.396904 1300 0.0975531 BAG-FAMILY MOLECULAR CHAPERONE REGULATOR-3 (BCL-2 BINDING ATHANOGENE- 3) (BAG-3) (BCL-2-BINDING PROTEIN BIS) (DOCKING PROTEIN CAIR-1). [SWISSPROT;Acc:O95817] BAG3 0.245785127
0.397328 716 0.105213 P28 ING5. [RefSeq;Acc:NM_032329] ING5 0.264801373
0.397415 3087 0.038802 FAM20A 0.097635972
0.397439 2113 0.0906856 "ORNITHINE AMINOTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.6.1.13) (ORNITHINE--OXO-ACID AMINOTRANSFERASE). [SWISSPROT;Acc:P04181]" OAT 0.22817489
0.399107 1737 0.094576 GLUTAMINYL-TRNA SYNTHASE (GLUTAMINE-HYDROLYZING)-LIKE 1. [RefSeq;Acc:NM_018292] QRSL1 0.236969033
0.399189 1285 0.0982055 GPR158 0.24601254
0.399468 2814 0.0780112 "ACYL-COA DEHYDROGENASE, VERY-LONG-CHAIN SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 1.3.99.-) (VLCAD). [SWISSPROT;Acc:P49748]" ACADVL 0.195287733
0.399507 1739 0.0946707 "URACIL-DNA GLYCOSYLASE, MITOCHONDRIAL PRECURSOR (EC 3.2.2.-) (UDG). [SWISSPROT;Acc:P13051]" UNG 0.236968814
1740 "PROBABLE GLUTAMYL-TRNA(GLN) AMIDOTRANSFERASE SUBUNIT B, MITOCHONDRIAL PRECURSOR (EC 6.3.5.-) (GLU-ADT SUBUNIT B) (CYTOCHROME OXIDASE ASSEMBLY FACTOR PET112 HOMOLOG). [SWISSPROT;Acc:O75879]" PET112L
0.399707 1738 0.0947181 FATTY-ACID AMIDE HYDROLASE (EC 3.1.-.-) (OLEAMIDE HYDROLASE) (ANANDAMIDE AMIDOHYDROLASE). [SWISSPROT;Acc:O00519] FAAH 0.23696883
0.401325 1028 0.101711 UBIQUITIN-LIKE PROTEIN SMT3A. [SWISSPROT;Acc:P55854] SUMO3 0.253437987
0.401402 1661 0.0958705 COPPER-TRANSPORTING ATPASE 2 (EC 3.6.3.4) (COPPER PUMP 2) (WILSON DISEASE-ASSOCIATED PROTEIN). [SWISSPROT;Acc:P35670] ATP7B 0.238839119
0.40158 2836 0.0775327 CALSYNTENIN-1 PRECURSOR. [SWISSPROT;Acc:O94985] CLSTN1 0.193069127
0.402189 2495 0.0866317 HISTIDINE DECARBOXYLASE (EC 4.1.1.22) (HDC). [SWISSPROT;Acc:P19113] HDC 0.215400471
0.402579 1134 0.10083 DOPACHROME TAUTOMERASE PRECURSOR (EC 5.3.3.12) (DT) (DCT) (DOPACHROME DELTA-ISOMERASE) (TYROSINASE-RELATED PROTEIN 2) (TRP-2) (TRP2). [SWISSPROT;Acc:P40126] DCT 0.250460158
0.403767 2496 0.0869714 ARMET PROTEIN PRECURSOR (ARGININE-RICH PROTEIN). [SWISSPROT;Acc:P55145] ARMET 0.215399971

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/