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 Gene Rank measured Hugo description final
Results: HTML CSV LaTeX Showing element 852 to 901 of 3206 in total
expected
Rank
measured
Hugo
description
final
0.256212 1025 0.0649343 ACRC ACRC PROTEIN; PUTATIVE NUCLEAR PROTEIN. [RefSeq;Acc:NM_052957] 0.25343973
0.256293 483 0.0703022 HNRNPA1 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1 (HELIX-DESTABILIZING PROTEIN) (SINGLE-STRAND BINDING PROTEIN) (HNRNP CORE PROTEIN A1). [SWISSPROT;Acc:P09651] 0.274304019
0.257167 1764 0.0607427 no value 0.236199435
0.257278 2191 0.0582372 YBX2 GERM CELL SPECIFIC Y-BOX BINDING PROTEIN; CONTRIN. [RefSeq;Acc:NM_015982] 0.226359036
0.257511 317 0.0750779 SRP9 SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN (SRP9). [SWISSPROT;Acc:P49458] 0.291552206
0.258242 1218 0.0640593 SNTA1 "ALPHA-1-SYNTROPHIN (59 KDA DYSTROPHIN-ASSOCIATED PROTEIN A1, ACIDIC COMPONENT 1) (PRO-TGF-ALPHA CYTOPLASMIC DOMAIN-INTERACTING PROTEIN 1) (TACIP1) (SYNTROPHIN 1). [SWISSPROT;Acc:Q13424]" 0.248059185
1900 0.0600275 MED28 ENDOTHELIAL-DERIVED GENE 1. [RefSeq;Acc:NM_025205] 0.232446697
0.25856 2170 0.0586994 CRBN PROTEIN X 0001. [RefSeq;Acc:NM_016302] 0.227024288
0.258646 2520 0.0555486 CYP2D6 CYTOCHROME P450 2D6 (EC 1.14.14.1) (CYPIID6) (P450-DB1) (DEBRISOQUINE 4-HYDROXYLASE). [SWISSPROT;Acc:P10635] 0.214766901
0.258811 2422 0.0564551 TCEA2 TRANSCRIPTION ELONGATION FACTOR A PROTEIN 2 (TRANSCRIPTION ELONGATION FACTOR S-II PROTEIN 2) (TESTIS-SPECIFIC S-II) (TRANSCRIPTION ELONGATION FACTOR TFIIS.L). [SWISSPROT;Acc:Q15560] 0.218132537
0.259184 1211 0.064293 AMOTL2 ANGIOMOTIN LIKE 2; LEMAN COILED-COIL PROTEIN; ANGIOMOTIN-LIKE PROTEIN 2. [RefSeq;Acc:NM_016201] 0.248059294
0.259665 2789 0.0519078 LYCAT 0.199902952
0.260164 601 0.0700114 ZNF503 0.269104872
0.261082 2259 0.0582358 RNF38 RING FINGER PROTEIN 38. [RefSeq;Acc:NM_022781] 0.223055592
0.2611 1643 0.0624093 DDI1 0.239024512
0.261739 2287 0.0581957 DLX2 HOMEOBOX PROTEIN DLX-2. [SWISSPROT;Acc:Q07687] 0.222342486
2288 MIZF MBD2 (METHYL-CPG-BINDING PROTEIN)-INTERACTING ZINC FINGER PROTEIN. [RefSeq;Acc:NM_015517]
0.261755 2236 0.0586323 IDH3B "ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT BETA, MITOCHONDRIAL PRECURSOR (EC 1.1.1.41) (ISOCITRIC DEHYDROGENASE) (NAD+-SPECIFIC ICDH). [SWISSPROT;Acc:O43837]" 0.223996867
0.261799 2682 0.0545554 EXOC2 EXOCYST COMPLEX COMPONENT SEC5. [SWISSPROT;Acc:Q96KP1] 0.208386587
0.261825 737 0.0692921 BCL6B "B-CELL CLL/LYMPHOMA 6, MEMBER B (ZINC FINGER PROTEIN); ZINC FINGER PROTEIN 62. [RefSeq;Acc:NM_181844]" 0.264650434
0.262124 2167 0.0595157 SPTLC1 SERINE PALMITOYLTRANSFERASE 1 (EC 2.3.1.50) (LONG CHAIN BASE BIOSYNTHESIS PROTEIN 1) (LCB 1) (SERINE-PALMITOYL-COA TRANSFERASE 1) (SPT 1) (SPT1). [SWISSPROT;Acc:O15269] 0.227051701
0.262913 2092 0.0601271 FDXR "NADPH:ADRENODOXIN OXIDOREDUCTASE, MITOCHONDRIAL PRECURSOR (EC 1.18.1.2) (ADRENODOXIN REDUCTASE) (AR) (FERREDOXIN-NADP(+) REDUCTASE). [SWISSPROT;Acc:P22570]" 0.228695804
0.262934 1001 0.0670247 TIMM10 MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM10. [SWISSPROT;Acc:Q9Y5J8] 0.254910738
0.262971 691 0.0698564 RPS6KA2 RIBOSOMAL PROTEIN S6 KINASE ALPHA 2 (EC 2.7.1.37) (S6K-ALPHA 2) (90 KDA RIBOSOMAL PROTEIN S6 KINASE 2) (P90-RSK 2) (RIBOSOMAL S6 KINASE 3) (RSK-3) (PP90RSK3). [SWISSPROT;Acc:Q15349] 0.26564298
0.263425 713 0.0697761 no value DJ153G14.2 (POSSIBLE CA BINDING PROTEIN SIMILAR TO NEFA) (FRAGMENT). [SPTREMBL;Acc:Q9UJN8] 0.264880326
0.26352 2582 0.0561617 BLOOD GROUP RH(CE) POLYPEPTIDE (RHESUS C/E ANTIGENS) (RH30A) (RHIXB) (RH POLYPEPTIDE 1) (RHPI). [SWISSPROT;Acc:P18577] 0.213121205
0.263668 2114 0.0601623 SGPL1 SPHINGOSINE-1-PHOSPHATE LYASE 1; SPHINGOSINE-1-PHOSPHATE LYASE. [RefSeq;Acc:NM_003901] 0.228174447
0.263715 794 0.0690966 GPR84 INFLAMMATION-RELATED G PROTEIN-COUPLED RECEPTOR EX33. [RefSeq;Acc:NM_020370] 0.2620124
795 PPT1 PALMITOYL-PROTEIN THIOESTERASE 1 PRECURSOR (EC 3.1.2.22) (PALMITOYL- PROTEIN HYDROLASE 1). [SWISSPROT;Acc:P50897]
796 C3orf60 SIMILAR TO NUCLEAR PROTEIN E3-3 ORF1. [SPTREMBL;Acc:Q9BU61]
0.264372 1447 0.064364 GARS GLYCYL-TRNA SYNTHETASE (EC 6.1.1.14) (GLYCINE--TRNA LIGASE) (GLYRS). [SWISSPROT;Acc:P41250] 0.243459973
0.264688 362 0.0741822 OSTF1 OSTEOCLAST STIMULATING FACTOR 1. [SWISSPROT;Acc:Q92882] 0.2802628
0.264963 2580 0.0564693 no value BLOOD GROUP RH(CE) POLYPEPTIDE (RHESUS C/E ANTIGENS) (RH30A) (RHIXB) (RH POLYPEPTIDE 1) (RHPI). [SWISSPROT;Acc:P18577] 0.213121455
2581 RHD BLOOD GROUP RH(D) POLYPEPTIDE (RHESUS D ANTIGEN) (RHXIII) (RH POLYPEPTIDE 2) (RHPII). [SWISSPROT;Acc:Q02161]
0.265419 334 0.0756863 ELOVL1 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 1 (CGI-88). [SWISSPROT;Acc:Q9BW60] 0.285157807
0.266132 1173 0.0663724 SMAD5 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 5 (SMAD 5) (MOTHERS AGAINST DPP HOMOLOG 5) (SMAD5) (HSMAD5) (JV5-1). [SWISSPROT;Acc:Q99717] 0.24939654
0.266211 2256 0.0593799 PIK3R1 PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY ALPHA SUBUNIT (PI3-KINASE P85-ALPHA SUBUNIT) (PTDINS-3-KINASE P85-ALPHA) (PI3K). [SWISSPROT;Acc:P27986] 0.223055772
0.266374 1756 0.063055 ATP6V1G1 VACUOLAR ATP SYNTHASE SUBUNIT G 1 (EC 3.6.3.14) (V-ATPASE G SUBUNIT 1) (VACUOLAR PROTON PUMP G SUBUNIT 1) (V-ATPASE 13 KDA SUBUNIT 1) (VACUOLAR ATP SYNTHASE SUBUNIT M16). [SWISSPROT;Acc:O75348] 0.236716046
0.266708 684 0.0708493 RPS6KA3 RIBOSOMAL PROTEIN S6 KINASE ALPHA 3 (EC 2.7.1.37) (S6K-ALPHA 3) (90 KDA RIBOSOMAL PROTEIN S6 KINASE 3) (P90-RSK 3) (RIBOSOMAL S6 KINASE 2) (RSK-2) (PP90RSK2) (INSULIN-STIMULATED PROTEIN KINASE 1) (ISPK-1). [SWISSPROT;Acc:P51812] 0.2656437
0.266776 3013 0.0325023 FRY 0.121833673
0.267389 3035 0.0306863 GTF2H1 TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX P62 SUBUNIT (BASIC TRANSCRIPTION FACTOR 62 KDA SUBUNIT) (BTF2-P62) (GENERAL TRANSCRIPTION FACTOR IIH POLYPEPTIDE 1). [SWISSPROT;Acc:P32780] 0.114762761
0.26764 2364 0.0589602 LMBR1 LIMB REGION 1 PROTEIN; LIMB REGION 1. [RefSeq;Acc:NM_022458] 0.220296667
0.267978 2253 0.0597741 PIK3R3 PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY GAMMA SUBUNIT (PI3-KINASE P85-GAMMA SUBUNIT) (PTDINS-3-KINASE P85-GAMMA) (P55PIK). [SWISSPROT;Acc:Q92569] 0.223055997
0.268263 2147 0.06101 TPT1 TRANSLATIONALLY CONTROLLED TUMOR PROTEIN (TCTP) (P23) (HISTAMINE- RELEASING FACTOR) (HRF). [SWISSPROT;Acc:P13693] 0.227426071
0.268301 571 0.0726249 KSR2 0.270684418
0.268503 2792 0.0536744 WDR32 0.199902422
0.26852 1210 0.0666089 SNTB2 "BETA-2-SYNTROPHIN (59 KDA DYSTROPHIN-ASSOCIATED PROTEIN A1, BASIC COMPONENT 2) (SYNTROPHIN 3) (SNT3) (SYNTROPHIN-LIKE) (SNTL). [SWISSPROT;Acc:Q13425]" 0.248059362
0.269336 2573 0.0574606 PRODH2 KIDNEY AND LIVER PROLINE OXIDASE 1. [RefSeq;Acc:NM_021232] 0.2133417
0.269399 1469 0.0654684 RELB TRANSCRIPTION FACTOR RELB (I-REL). [SWISSPROT;Acc:Q01201] 0.243016492
0.269788 1884 0.0627928 FMO6P PUTATIVE DIMETHYLANILINE MONOOXYGENASE [N-OXIDE FORMING] 6 (EC 1.14.13.8) (FLAVIN-CONTAINING MONOOXYGENASE 6) (FMO 6) (DIMETHYLANILINE OXIDASE 6). [SWISSPROT;Acc:O60774] 0.232748677

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/