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 [...,...].
measured Gene Rank description expected Hugo final
Results: HTML CSV LaTeX Showing element 702 to 751 of 3206 in total
measured
Rank
description
expected
Hugo
final
0.0453043 2382 PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FES/FPS (EC 2.7.1.112) (C-FES). [SWISSPROT;Acc:P07332] 0.206215 FES 0.219694494
0.0454701 2677 GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE (EC 2.7.7.12) (GAL-1-P URIDYLYLTRANSFERASE) (UDP-GLUCOSE--HEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE). [SWISSPROT;Acc:P07902] 0.217847 no value 0.208724931
0.0454705 3081 CARBOXYPEPTIDASE B PRECURSOR. [RefSeq;Acc:NM_020361] 0.454991 CPA6 0.099937142
0.0455028 3174 NUCLEAR RNA EXPORT FACTOR 5 (TAP-LIKE PROTEIN 1) (TAPL-1). [SWISSPROT;Acc:Q9H1B4] 0.820367 NXF5 0.055466395
0.0457909 871 T-CELL LEUKEMIA HOMEOBOX PROTEIN 3 (HOMEOBOX PROTEIN HOX-11L2). [SWISSPROT;Acc:O43711] 0.175939 TLX3 0.260265774
0.0460179 370 "COFILIN, NON-MUSCLE ISOFORM (18 KDA PHOSPHOPROTEIN) (P18). [SWISSPROT;Acc:P23528]" 0.164816 CFL1 0.279207723
371 DESTRIN (ACTIN-DEPOLYMERIZING FACTOR) (ADF). [SWISSPROT;Acc:P18282] DSTN
372 "COFILIN, MUSCLE ISOFORM (COFILIN 2). [SWISSPROT;Acc:Q9Y281]" CFL2
0.0460867 764 POTENTIAL PHOSPHOLIPID-TRANSPORTING ATPASE IIA (EC 3.6.1.-). [SWISSPROT;Acc:O75110] 0.174809 ATP9A 0.263640316
765 GAMMA-SNAP-ASSOCIATED FACTOR 1; RAB11-INTERACTING PROTEIN. [RefSeq;Acc:NM_015470] RAB11FIP5
0.0461397 1799 0.196587 FAM57B 0.234703719
0.0461407 2611 TOPOISOMERASE (DNA) II BINDING PROTEIN. [RefSeq;Acc:NM_007027] 0.218331 TOPBP1 0.211333709
0.0462274 1865 DYNACTIN 4. [RefSeq;Acc:NM_032486] 0.198227 DCTN5 0.233204357
0.0462548 286 "FATTY ACID-BINDING PROTEIN, HEART (H-FABP) (MUSCLE FATTY ACID-BINDING PROTEIN) (M-FABP) (MAMMARY-DERIVED GROWTH INHIBITOR) (MDGI). [SWISSPROT;Acc:P05413]" 0.153258 FABP3 0.30181002
0.046337 2600 UBIQUITIN-ACTIVATING ENZYME E1 (A1S9 PROTEIN). [SWISSPROT;Acc:P22314] 0.217657 UBE1 0.212890006
0.0463914 2182 SERINE/THREONINE-PROTEIN KINASE PAK 2 (EC 2.7.1.-) (P21-ACTIVATED KINASE 2) (PAK-2) (PAK65) (GAMMA-PAK) (S6/H4 KINASE). [SWISSPROT;Acc:Q13177] 0.204773 PAK2 0.226550375
0.046465 2134 NEUROPILIN- AND TOLLOID-LIKE PROTEIN 1 ISOFORM 3 PRECURSOR. [RefSeq;Acc:NM_138966] 0.203814 NETO1 0.22797747
0.0465063 1145 0.185855 TMEM132D 0.250228942
0.0465225 2362 "SOLUTE CARRIER FAMILY 20 (PHOSPHATE TRANSPORTER), MEMBER 1; GLVR-1; PIT-1; GIBBON APE LEUKEMIA VIRUS RECEPTOR 1. [RefSeq;Acc:NM_005415]" 0.211181 SLC20A1 0.220296807
0.0466014 2656 SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 1. [SWISSPROT;Acc:O15126] 0.221972 SCAMP1 0.209942695
0.0467541 1562 0.193844 ARRDC3 0.241194466
0.046789 549 SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH PROTEIN (SH3BGR PROTEIN) (21- GLUTAMIC ACID-RICH PROTEIN) (21-GARP). [SWISSPROT;Acc:P55822] 0.172653 SH3BGR 0.271000214
550 LATS HOMOLOG 1. [RefSeq;Acc:NM_004690] LATS1
551 TBC1 DOMAIN FAMILY PROTEIN C22ORF4. [SWISSPROT;Acc:Q8WUA7] TBC1D22A
552 NUCLEAR RECEPTOR COACTIVATOR 7; ESTROGEN RECEPTOR ASSOCIATED PROTEIN 140 KDA. [RefSeq;Acc:NM_181782] NCOA7
0.0468234 1404 EPSIN 3. [RefSeq;Acc:NM_017957] 0.191876 EPN3 0.244029477
0.046965 101 "INOSITOL POLYPHOSPHATE-4-PHOSPHATASE, TYPE II, 105KD; INOSITOL POLYPHOSPHATE 4-PHOSPHATASE II; 4-PHOSPHATASE II. [RefSeq;Acc:NM_003866]" 0.125644 INPP4B 0.373794212
0.0469672 3173 NUCLEAR RNA EXPORT FACTOR 3 (TAP-LIKE PROTEIN 3) (TAPL-3). [SWISSPROT;Acc:Q9H4D5] 0.846512 NXF3 0.055483206
0.0470468 2781 PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN (EC 6.1.1.20) (PHENYLALANINE-- TRNA LIGASE BETA CHAIN) (PHERS) (HSPC173). [SWISSPROT;Acc:Q9NSD9] 0.234118 FARSB 0.200953365
0.0471496 1350 ZINC FINGER PROTEIN 40 (HUMAN IMMUNODEFICIENCY VIRUS TYPE I ENHANCER- BINDING PROTEIN 1) (HIV-EP1) (MAJOR HISTOCOMPATIBILITY COMPLEX BINDING PROTEIN 1) (MBP-1) (POSITIVE REGULATORY DOMAIN II BINDING FACTOR 1) (PRDII-BF1). [SWISSPROT;Acc:P15822] 0.192302 HIVEP1 0.245185177
0.0471781 2063 BECLIN 1 (COILED-COIL MYOSIN-LIKE BCL2-INTERACTING PROTEIN) (PROTEIN GT197). [SWISSPROT;Acc:Q14457] 0.20547 BECN1 0.229610649
0.0473076 1288 ZINC FINGER-LIKE PROTEIN 9. [RefSeq;Acc:NM_033414] 0.192307 ZNF622 0.246000406
0.0474703 389 SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN D2; RSC6P; MAMMALIAN CHROMATIN REMODELING COMPLEX BRG1-ASSOCIATED FACTOR 60B; SWP73-LIKE PROTEIN; CHROMATIN REMODELING COMPLEX BAF60B SUBUNIT; SWI/SNF COMPLEX 60 KDA SUBUNIT B. [Sour 0.170299 SMARCD2 0.278746792
0.0476371 3185 1.01816 CCDC104 0.04678744
0.0476698 2123 0.208966 TCP11L2 0.228122278
0.0476887 1686 SORTING NEXIN 17. [SWISSPROT;Acc:Q15036] 0.200292 SNX17 0.23809588
0.0479426 403 CENTAURIN GAMMA 2. [SWISSPROT;Acc:Q9UPQ3] 0.172299 CENTG2 0.27825234
0.0480412 516 0.176368 METT10D 0.272391817
0.0480531 2658 "SOLUTE CARRIER FAMILY 13, MEMBER 4 (NA+/SULFATE COTRANSPORTER SUT-1). [SWISSPROT;Acc:Q9UKG4]" 0.228892 SLC13A4 0.209937875
0.0480742 380 CALCYPHOSINE. [SWISSPROT;Acc:Q13938] 0.172225 CAPS 0.279136014
0.0481673 2659 "SOLUTE CARRIER FAMILY 13, MEMBER 1 (RENAL SODIUM/SULFATE COTRANSPORTER) (NA(+)/SULFATE COTRANSPORTER) (HNASI-1). [SWISSPROT;Acc:Q9BZW2]" 0.229436 SLC13A1 0.209937848
0.0483159 561 POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2; UDP-GALNAC TRANSFERASE 2. [RefSeq;Acc:NM_004481] 0.178411 GALNT2 0.270812338
0.0483186 356 0.171674 no value 0.281455549
0.0483307 1915 TYROSYL-TRNA SYNTHETASE (EC 6.1.1.1) (TYROSYL--TRNA LIGASE) (TYRRS). [SWISSPROT;Acc:P54577] 0.208298 YARS 0.232026712
0.0485005 444 CYTOCHROME C-TYPE HEME LYASE (EC 4.4.1.17) (CCHL) (HOLOCYTOCHROME C- TYPE SYNTHASE). [SWISSPROT;Acc:P53701] 0.17528 HCCS 0.27670299
0.048504 197 "POLYMERASE (DNA DIRECTED) IOTA; RAD30 (S. CEREVISIAE) HOMOLOG B; POLYMERASE (DNA-DIRECTED), IOTA. [RefSeq;Acc:NM_007195]" 0.150395 POLI 0.322510722
0.0485629 3059 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-2 SUBUNIT (ADENYLATE CYCLASE-INHIBITING G ALPHA PROTEIN). [SWISSPROT;Acc:P04899]" 0.460606 GNAI2 0.105432626
0.048624 3089 0.498014 TM4SF19 0.097635809
3090 METHYLTRANSFERASE LIKE 2. [RefSeq;Acc:NM_018396] no value
3091 METTL2A

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/