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 101 to 150 of 3206 in total
measured
Rank
description
expected
Hugo
final
0.0225037 1083 POTENTIAL PHOSPHOLIPID-TRANSPORTING ATPASE IH (EC 3.6.3.1) (ATPASE CLASS I TYPE 11A) (ATPASE IS). [SWISSPROT;Acc:P98196] 0.0892747 ATP11A 0.252072536
0.0225884 2994 HEPARAN SULFATE D-GLUCOSAMINYL 3-O-SULFOTRANSFERASE 3B1. [RefSeq;Acc:NM_006041] 0.166906 HS3ST3B1 0.135336057
0.0227421 2138 CD109; GOV SYSTEM ALLOANTIGENS ON PLATELETS. [RefSeq;Acc:NM_133493] 0.0998232 CD109 0.227823792
0.0228794 3041 MITOCHONDRIAL SOLUTE CARRIER PROTEIN. [RefSeq;Acc:NM_145305] 0.208398 SLC25A43 0.109787042
0.0228851 3193 PROTEIN HSPC134 (PROTEIN CDA04). [SWISSPROT;Acc:Q9BY43] 0.620827 CHMP4A 0.036862282
0.0229678 3190 "PROTEIN PHOSPHATASE 1, REGULATORY SUBUNIT 14D; PKC-DEPENDENT PP1 INHIBITORY PROTEIN. [RefSeq;Acc:NM_017726]" 0.615511 PPP1R14D 0.037315011
0.0229997 524 "GLYCOGEN PHOSPHORYLASE, MUSCLE FORM (EC 2.4.1.1) (MYOPHOSPHORYLASE). [SWISSPROT;Acc:P11217]" 0.0845876 PYGM 0.27190392
0.0230825 2771 MAWD BINDING PROTEIN (UNKNOWN PROTEIN 32 FROM 2D-PAGE OF LIVER TISSUE). [SWISSPROT;Acc:P30039] 0.11461 PBLD 0.201400401
2772 LYSOPHOSPHOLIPASE I; LYSOPHOSPHOLIPASE 1; LYSOPHOSPHOLIPID-SPECIFIC LYSOPHOSPHOLIPASE; ACYL-PROTEIN THIOESTERASE-1. [RefSeq;Acc:NM_006330] LYPLA1
0.0231389 3012 CD209 ANTIGEN; DENDRITIC CELL-SPECIFIC ICAM3-GRABBING NONINTEGRIN. [RefSeq;Acc:NM_021155] 0.189922 CD209 0.1218337
0.0231429 525 "GLYCOGEN PHOSPHORYLASE, BRAIN FORM (EC 2.4.1.1). [SWISSPROT;Acc:P11216]" 0.0851144 PYGB 0.271903462
0.0233268 2734 VESICLE-ASSOCIATED MEMBRANE PROTEIN 1 (VAMP-1) (SYNAPTOBREVIN 1). [SWISSPROT;Acc:P23763] 0.113606 VAMP1 0.205330704
0.023532 1975 0.101818 DAGLA 0.23111827
0.0238444 1684 60S RIBOSOMAL PROTEIN L37 (G1.16). [SWISSPROT;Acc:P02403] 0.100146 RPL37 0.238096379
1685 "SPLICING FACTOR, ARGININE/SERINE-RICH 1 (PRE-MRNA SPLICING FACTOR SF2, P33 SUBUNIT) (ALTERNATIVE SPLICING FACTOR ASF-1). [SWISSPROT;Acc:Q07955]" SFRS1
0.0239451 3194 0.649583 CHMP4C 0.036862264
0.0240186 2212 NUCLEOBINDIN 1 PRECURSOR (CALNUC). [SWISSPROT;Acc:Q02818] 0.106724 NUCB1 0.225053409
0.0240826 2533 KERATIN ASSOCIATED PROTEIN 2-4; KERATIN ASSOCIATED PROTEIN 2.4. [RefSeq;Acc:NM_033184] 0.112137 no value 0.214760516
0.0241104 656 BAI1-ASSOCIATED PROTEIN 3; BAI-ASSOCIATED PROTEIN 3. [RefSeq;Acc:NM_003933] 0.0901025 BAIAP3 0.26758858
0.0241725 2621 RHO-GTPASE-ACTIVATING PROTEIN 7 (RHO-TYPE GTPASE-ACTIVATING PROTEIN 7) (DELETED IN LIVER CANCER 1 PROTEIN) (DLC-1) (HP PROTEIN) (STAR-RELATED LIPID TRANSFER PROTEIN 12) (STARD12) (START DOMAIN-CONTAINING PROTEIN 12). [SWISSPROT;Acc:Q96QB1] 0.115107 DLC1 0.210000261
0.0241785 2623 SPHINGOSINE KINASE 1 (EC 2.7.1.-) (SK 1) (SPK 1). [SWISSPROT;Acc:Q9NYA1] 0.115136 SPHK1 0.209999479
2624 SPHINGOSINE KINASE 2 (EC 2.7.1.-) (SK 2) (SPK 2). [SWISSPROT;Acc:Q9NRA0] SPHK2
0.0241928 3188 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 14A; 17-KDA PKC-POTENTIATED INHIBITORY PROTEIN OF PP1. [RefSeq;Acc:NM_033256]" 0.648338 PPP1R14A 0.037315104
0.0241952 3181 CULLIN HOMOLOG 2 (CUL-2). [SWISSPROT;Acc:Q13617] 0.486077 CUL2 0.049776476
0.0241982 3038 PANTOTHENATE KINASE 1 (EC 2.7.1.33) (PANTOTHENIC ACID KINASE 1) (HPANK1) (HPANK). [SWISSPROT;Acc:Q8TE04] 0.22041 PANK1 0.109787215
3039 "28S RIBOSOMAL PROTEIN S17, MITOCHONDRIAL PRECURSOR (MRP-S17) (HSPC011). [SWISSPROT;Acc:Q9Y2R5]" MRPS17
0.0242456 882 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] 0.0932247 PIK3C2G 0.260076997
0.024304 2905 0.139564 PLEKHG2 0.174142329
0.0243256 1931 0.104981 FAM98B 0.23171431
0.0243642 2116 0.106779 DPY19L2P2 0.228174079
0.0244129 2410 0.111754 VPS8 0.218452136
0.0244744 2319 LEUKOCYTE ELASTASE INHIBITOR (LEI) (MONOCYTE/NEUTROPHIL ELASTASE INHIBITOR) (M/NEI) (EI). [SWISSPROT;Acc:P30740] 0.110346 SERPINB1 0.221796893
0.0244747 2713 LAMIN B RECEPTOR (INTEGRAL NUCLEAR ENVELOPE INNER MEMBRANE PROTEIN) (LMN2R). [SWISSPROT;Acc:Q14739] 0.11804 LBR 0.207342426
0.0245797 1286 0.0999171 ISCA1 0.246000935
0.0246707 2638 TRANSFORMING PROTEIN RHOA (H12). [SWISSPROT;Acc:P06749] 0.117481 RHOA 0.209997361
2639 3-MERCAPTOPYRUVATE SULFURTRANSFERASE (EC 2.8.1.2) (MST). [SWISSPROT;Acc:P25325] MPST
2640 AARSD1
0.0247366 1320 THIOREDOXIN DOMAIN-CONTAINING 2; SPERM-SPECIFIC THIOREDOXIN; THIOREDOXIN DOMAIN-CONTAINING 2 (SPERMATOZOA). [RefSeq;Acc:NM_032243] 0.100732 TXNDC2 0.245568439
0.0247893 3015 CD209 ANTIGEN-LIKE; PUTATIVE TYPE II MEMBRANE PROTEIN. [RefSeq;Acc:NM_014257] 0.203469 CLEC4M 0.121833301
0.024834 1782 17 BETA-HYDROXYSTEROID DEHYDROGENASE. [SPTREMBL;Acc:Q13034] 0.105517 no value 0.23535544
0.0249116 526 MYOSIN XV (UNCONVENTIONAL MYOSIN-15). [SWISSPROT;Acc:Q9UKN7] 0.0916194 MYO15A 0.271903112
527 "GLYCOGEN PHOSPHORYLASE, LIVER FORM (EC 2.4.1.1). [SWISSPROT;Acc:P06737]" PYGL
0.0249219 2414 TUMOR DIFFERENTIALLY EXPRESSED PROTEIN 2. [RefSeq;Acc:NM_178865] 0.114139 SERINC2 0.218346928
0.0249248 2674 CELL ADHESION MOLECULE WITH HOMOLOGY TO L1CAM PRECURSOR; NEURAL CELL ADHESION MOLECULE; CELL ADHESION MOLECULE L1-LIKE; L1 CELL ADHESION MOLECULE 2. [RefSeq;Acc:NM_006614] 0.119125 CHL1 0.209232319
0.0249436 1440 "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]" 0.102427 AKT3 0.243525633
0.0249538 2535 "KERATIN, ULTRA HIGH-SULFUR MATRIX PROTEIN B (UHS KERATIN B) (UHS KERB). [SWISSPROT;Acc:O75690]" 0.116194 KRTAP5-8 0.214759798
0.0249741 2532 KERATIN ASSOCIATED PROTEIN 1.5. [RefSeq;Acc:NM_031957] 0.116288 no value 0.214760766
0.0250043 3024 SYNBINDIN (TRS23 HOMOLOG) (HEMATOPOIETIC STEM/PROGENITOR CELL PROTEIN 172) (HSPC172) (PTD009) (CGI-104). [SWISSPROT;Acc:Q9Y296] 0.209553 0.119322081
3025 SEDLIN. [SWISSPROT;Acc:O14582] ZNF547
0.0250957 2530 "KERATIN, ULTRA HIGH-SULFUR MATRIX PROTEIN A (UHS KERATIN A) (UHS KERA). [SWISSPROT;Acc:P26371]" 0.116854 no value 0.214761155

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/