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

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/