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 description Rank final Hugo Gene measured
Results: HTML CSV LaTeX Showing element 51 to 100 of 3206 in total
expected
description
Rank
final
Hugo
measured
0.0901539 NOSTRIN. [RefSeq;Acc:NM_052946] 1730 0.237039108 NOSTRIN 0.02137
0.0901743 T-BOX TRANSCRIPTION FACTOR TBX6 (T-BOX PROTEIN 6). [SWISSPROT;Acc:O95947] 2695 0.207986089 TBX6 0.018755
0.0901805 STAR-RELATED LIPID TRANSFER PROTEIN 8 (STARD8) (START DOMAIN- CONTAINING PROTEIN 8). [SWISSPROT;Acc:Q92502] 2633 0.209998836 STARD8 0.0189378
0.0905944 CYTOPLASMIC ANTIPROTEINASE 3 (CAP3) (CAP-3) (PROTEASE INHIBITOR 9) (SERPIN B9). [SWISSPROT;Acc:P50453] 2321 0.22179627 SERPINB9 0.0200935
0.0908932 RAS-RELATED PROTEIN RAB-37. [SWISSPROT;Acc:Q96AX2] 2068 0.229451708 RAB37 0.0208556
0.0909983 CLEFT LIP AND PALATE ASSOCIATED TRANSMEMBRANE PROTEIN 1. [RefSeq;Acc:NM_001294] 2162 0.227243806 CLPTM1 0.0206788
0.0912429 CARBOXYPEPTIDASE A1 PRECURSOR (EC 3.4.17.1). [SWISSPROT;Acc:P15085] 1810 0.234430295 CPA1 0.0213901
0.0914656 "NEUTRAL AND BASIC AMINO ACID TRANSPORT PROTEIN RBAT (B(0,+)-TYPE AMINO ACID TRANSPORT PROTEIN) (NBAT) (D2H). [SWISSPROT;Acc:Q07837]" 1812 0.234430212 SLC3A1 0.0214423
0.0916194 "GLYCOGEN PHOSPHORYLASE, LIVER FORM (EC 2.4.1.1). [SWISSPROT;Acc:P06737]" 527 0.271903112 PYGL 0.0249116
MYOSIN XV (UNCONVENTIONAL MYOSIN-15). [SWISSPROT;Acc:Q9UKN7] 526 MYO15A
0.0920202 REGULATOR OF G-PROTEIN SIGNALING 19 (RGS19) (G-ALPHA INTERACTING PROTEIN) (GAIP PROTEIN). [SWISSPROT;Acc:P49795] 2932 0.158415218 RGS19 0.0145774
0.0922076 "RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 3; RHOGEF PROTEIN; 59.8 KDA PROTEIN; EXCHANGE FACTOR FOUND IN PLATELETS AND LEUKEMIC AND NEURONAL TISSUES, XPLN. [RefSeq;Acc:NM_019555]" 1527 0.242317336 ARHGEF3 0.0223435
0.0927234 ZINC FINGER PROTEIN GLI3. [SWISSPROT;Acc:P10071] 2360 0.220297142 GLI3 0.0204267
0.0932247 PHOSPHATIDYLINOSITOL-4-PHOSPHATE 3-KINASE C2 DOMAIN-CONTAINING GAMMA POLYPEPTIDE (EC 2.7.1.154) (PHOSPHOINOSITIDE 3-KINASE-C2-GAMMA) (PTDINS-3-KINASE C2 GAMMA) (PI3K-C2GAMMA). [SWISSPROT;Acc:O75747] 882 0.260076997 PIK3C2G 0.0242456
0.0932586 REGULATOR OF G-PROTEIN SIGNALING 17 (RGS17). [SWISSPROT;Acc:Q9UGC6] 2930 0.158415417 RGS17 0.0147736
0.0936986 485 0.274303992 CHCHD3 0.0257019
0.0938936 STAR-RELATED LIPID TRANSFER PROTEIN 13 (STARD13) (START DOMAIN- CONTAINING PROTEIN 13) (46H23.2). [SWISSPROT;Acc:Q9Y3M8] 2625 0.209999404 STARD13 0.0197176
0.0939662 PUTATIVE RNA-BINDING PROTEIN 15 (RNA BINDING MOTIF PROTEIN 15) (ONE-TWENTY TWO PROTEIN). [SWISSPROT;Acc:Q96T37] 2929 0.158415473 RBM15 0.0148857
0.0940277 2598 0.212890457 HHATL 0.0200176
0.0944225 DELTA 1-PYRROLINE-5-CARBOXYLATE SYNTHETASE (P5CS) [INCLUDES: GLUTAMATE 5-KINASE (EC 2.7.2.11) (GAMMA-GLUTAMYL KINASE) (GK); GAMMA-GLUTAMYL PHOSPHATE REDUCTASE (GPR) (EC 1.2.1.41) (GLUTAMATE-5-SEMIALDEHYDE DEHYDROGENASE) (GLUTAMYL-GAMMA-SEMIALDEHYDE DEHYDR 1681 0.238166751 ALDH18A1 0.0224883
0.0946679 DELTA(14)-STEROL REDUCTASE (EC 1.3.1.70) (C-14 STEROL REDUCTASE) (STEROL C14-REDUCTASE) (DELTA14-SR) (TRANSMEMBRANE 7 SUPERFAMILY MEMBER 2) (ANOTHER NEW GENE 1) (PUTATIVE STEROL REDUCTASE SR-1). [SWISSPROT;Acc:O76062] 2712 0.207342721 TM7SF2 0.0196287
0.0950179 STROMAL CELL-DERIVED FACTOR 2-LIKE PROTEIN 1 PRECURSOR (SDF2 LIKE PROTEIN 1) (PWP1-INTERACTING PROTEIN 8). [SWISSPROT;Acc:Q9HCN8] 1890 0.232722466 SDF2L1 0.0221128
0.0954818 APOPAIN PRECURSOR (EC 3.4.22.-) (CYSTEINE PROTEASE CPP32) (YAMA PROTEIN) (CPP-32) (CASPASE-3) (CASP-3) (SREBP CLEAVAGE ACTIVITY 1) (SCA-1). [SWISSPROT;Acc:P42574] 1829 0.234085449 CASP3 0.0223509
0.0959121 TRANSCRIPTION FACTOR LBX1. [SWISSPROT;Acc:P52954] 2927 0.158415883 LBX1 0.015194
0.0959445 2141 0.227823377 ZC3H12C 0.0218584
0.0962388 BA304I5.1 (NOVEL LIPASE) (FRAGMENT). [SPTREMBL;Acc:Q96LG2] 1849 0.233451581 LIPM 0.0224671
0.0965355 "ZINC FINGER PROTEIN 289, ID1 REGULATED; LIKELY ORTHOLOG OF MOUSE ZFP289. [RefSeq;Acc:NM_032389]" 489 0.274303236 ZNF289 0.02648
0.0966924 HYALURONAN SYNTHASE 3 (EC 2.4.1.212) (HYALURONATE SYNTHASE 3) (HYALURONIC ACID SYNTHASE 3) (HA SYNTHASE 3). [SWISSPROT;Acc:O00219] 1991 0.230850615 HAS3 0.0223215
0.0967906 "MYOSIN LIGHT CHAIN 1, SLOW-TWITCH MUSCLE B/VENTRICULAR ISOFORM (MLC1SB) (ALKALI). [SWISSPROT;Acc:P08590]" 819 0.26132703 MYL3 0.025294
0.0975853 "MYOSIN LIGHT CHAIN 1, SKELETAL MUSCLE ISOFORM (MLC1F) (A1 CATALYTIC) (ALKALI). [SWISSPROT;Acc:P05976]" 821 0.261326245 MYL1 0.0255016
0.0977138 2543 0.214613494 FAM86C 0.0209707
0.0991465 "MYOSIN LIGHT CHAIN 1, EMBRYONIC MUSCLE/ATRIAL ISOFORM (PRO1957). [SWISSPROT;Acc:P12829]" 820 0.261326421 no value 0.0259096
0.0998232 CD109; GOV SYSTEM ALLOANTIGENS ON PLATELETS. [RefSeq;Acc:NM_133493] 2138 0.227823792 CD109 0.0227421
0.0999171 1286 0.246000935 ISCA1 0.0245797
0.100146 "SPLICING FACTOR, ARGININE/SERINE-RICH 1 (PRE-MRNA SPLICING FACTOR SF2, P33 SUBUNIT) (ALTERNATIVE SPLICING FACTOR ASF-1). [SWISSPROT;Acc:Q07955]" 1685 0.238096379 SFRS1 0.0238444
60S RIBOSOMAL PROTEIN L37 (G1.16). [SWISSPROT;Acc:P02403] 1684 RPL37
0.100647 DJ570F3.6 (NOVEL PROTEIN SIMILAR TO LYSOPHOSPHOLIPASE II (LYPLA2)). [SPTREMBL;Acc:Q9UGE0] 2773 0.201399942 no value 0.0202703
0.100732 THIOREDOXIN DOMAIN-CONTAINING 2; SPERM-SPECIFIC THIOREDOXIN; THIOREDOXIN DOMAIN-CONTAINING 2 (SPERMATOZOA). [RefSeq;Acc:NM_032243] 1320 0.245568439 TXNDC2 0.0247366
0.101375 2541 0.214614057 no value 0.0217565
0.101818 1975 0.23111827 DAGLA 0.023532
0.101841 ALPHA/BETA HYDROLASE DOMAIN CONTAINING PROTEIN 1 ISOFORM 2; LUNG ALPHA/BETA HYDROLASE PROTEIN 1. [RefSeq;Acc:NM_152870] 953 0.256404591 ABHD1 0.0261125
0.10215 THIOSULFATE SULFURTRANSFERASE (EC 2.8.1.1) (RHODANESE). [SWISSPROT;Acc:Q16762] 2641 0.209997063 TST 0.0214512
0.102213 PHOSPHATIDYLINOSITOL-4-PHOSPHATE 3-KINASE C2 DOMAIN-CONTAINING BETA POLYPEPTIDE (EC 2.7.1.154) (PHOSPHOINOSITIDE 3-KINASE-C2-BETA) (PTDINS-3-KINASE C2 BETA) (PI3K-C2BETA) (C2-PI3K). [SWISSPROT;Acc:O00750] 883 0.260076507 PIK3C2B 0.0265832
0.102351 NEIGHBOR OF COX4. [SWISSPROT;Acc:O43402] 769 0.263638851 COX4NB 0.0269837
0.102427 "RAC-GAMMA SERINE/THREONINE PROTEIN KINASE (EC 2.7.1.-) (RAC-PK-GAMMA) (PROTEIN KINASE AKT-3) (PROTEIN KINASE B, GAMMA) (PKB GAMMA) (STK-2). [SWISSPROT;Acc:Q9Y243]" 1440 0.243525633 AKT3 0.0249436
0.102457 LYSOPHOSPHOLIPASE II; ACYL-PROTEIN THIOESTERASE. [RefSeq;Acc:NM_007260] 2774 0.201399612 LYPLA2P1 0.0206348
0.102605 DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 31 ISOFORM 1; DEAD/DEXH HELICASE DDX31. [RefSeq;Acc:NM_022779] 1231 0.247782272 DDX31 0.0254237
0.102768 T-BOX TRANSCRIPTION FACTOR TBX19 (T-BOX PROTEIN 19). [SWISSPROT;Acc:O60806] 2452 0.216859334 TBX19 0.0222862
0.102796 TRANSFORMING PROTEIN RHOC (H9). [SWISSPROT;Acc:P08134] 2636 0.209997471 RHOC 0.0215869
0.104626 ENIGMA PROTEIN; LIM DOMAIN PROTEIN. [RefSeq;Acc:NM_005451] 504 0.274067631 no value 0.0286746

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/