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 [...,...].
expected Rank Gene description measured final Hugo
Results: HTML CSV LaTeX Showing element 151 to 200 of 3206 in total
expected
Rank
description
measured
final
Hugo
0.115136 2624 SPHINGOSINE KINASE 2 (EC 2.7.1.-) (SK 2) (SPK 2). [SWISSPROT;Acc:Q9NRA0] 0.0241785 0.209999479 SPHK2
0.115356 1516 DNA REPLICATION LICENSING FACTOR MCM3 (DNA POLYMERASE ALPHA HOLOENZYME-ASSOCIATED PROTEIN P1) (RLF BETA SUBUNIT) (P102 PROTEIN) (P1-MCM3). [SWISSPROT;Acc:P25205] 0.0279589 0.242370575 MCM3
0.11537 1647 0.0275762 0.23902401 no value
0.115399 2356 ZINC FINGER PROTEIN GLI1 (GLIOMA-ASSOCIATED ONCOGENE) (ONCOGENE GLI). [SWISSPROT;Acc:P08151] 0.0254221 0.220297403 GLI1
2357 ZINC FINGER PROTEIN GLI2 (TAX HELPER PROTEIN). [SWISSPROT;Acc:P10070] GLI2
0.115441 2405 INTEGRAL MEMBRANE PROTEIN 2A (E25 PROTEIN). [SWISSPROT;Acc:O43736] 0.0252512 0.218736844 ITM2A
0.115449 1257 SERINE/THREONINE PROTEIN KINASE 12 (EC 2.7.1.37) (AURORA- AND IPL1- LIKE MIDBODY-ASSOCIATED PROTEIN 1) (AIM-1) (AURORA/IPL1-RELATED KINASE 2) (AURORA-RELATED KINASE 2) (STK-1) (AURORA-B). [SWISSPROT;Acc:Q96GD4] 0.0285544 0.247333455 AURKB
0.116194 2535 "KERATIN, ULTRA HIGH-SULFUR MATRIX PROTEIN B (UHS KERATIN B) (UHS KERB). [SWISSPROT;Acc:O75690]" 0.0249538 0.214759798 KRTAP5-8
0.116238 830 KETOHEXOKINASE (EC 2.7.1.3) (HEPATIC FRUCTOKINASE). [SWISSPROT;Acc:P50053] 0.0303497 0.26109964 KHK
0.116288 2532 KERATIN ASSOCIATED PROTEIN 1.5. [RefSeq;Acc:NM_031957] 0.0249741 0.214760766 no value
0.116515 808 0.0305282 0.2620109 TMCC1
0.116699 276 ENTEROPEPTIDASE PRECURSOR (EC 3.4.21.9) (ENTEROKINASE). [SWISSPROT;Acc:P98073] 0.0355659 0.304766108 PRSS7
0.116854 2530 "KERATIN, ULTRA HIGH-SULFUR MATRIX PROTEIN A (UHS KERATIN A) (UHS KERA). [SWISSPROT;Acc:P26371]" 0.0250957 0.214761155 no value
0.116875 730 ZINC FINGER PROTEIN 261 (DXS6673E PROTEIN). [SWISSPROT;Acc:Q14202] 0.030934 0.264675936 ZMYM3
0.117061 2406 INTEGRAL MEMBRANE PROTEIN 2C (TRANSMEMBRANE PROTEIN BRI3) (NPD018). [SWISSPROT;Acc:Q9NQX7] 0.0256055 0.218736385 ITM2C
0.117481 2638 TRANSFORMING PROTEIN RHOA (H12). [SWISSPROT;Acc:P06749] 0.0246707 0.209997361 RHOA
2639 3-MERCAPTOPYRUVATE SULFURTRANSFERASE (EC 2.8.1.2) (MST). [SWISSPROT;Acc:P25325] MPST
2640 AARSD1
0.117581 1854 0.0274494 0.233450983 no value
0.117689 2375 THIAMIN PYROPHOSPHOKINASE 1; MOUSE THIAMIN PYROPHOSPHOKINASE HOMOLOG; THIAMINE PYROPHOSPHOKINASE. [RefSeq;Acc:NM_022445] 0.0258973 0.220048603
0.117755 731 ZINC FINGER PROTEIN 198 (FUSED IN MYELOPROLIFERATIVE DISORDERS PROTEIN) (REARRANGED IN ATYPICAL MYELOPROLIFERATIVE DISORDER PROTEIN). [SWISSPROT;Acc:Q9UBW7] 0.0311669 0.26467581 ZMYM2
0.117865 1855 PRESENILIN-LIKE PROTEIN 2 (EC 3.4.99.-) (SPPL2A PROTEIN). [SWISSPROT;Acc:Q8TCT8] 0.0275157 0.233450982 no value
0.117937 2933 REGULATOR OF G-PROTEIN SIGNALING 20 (RGS20) (REGULATOR OF GZ- SELECTIVE PROTEIN SIGNALING 1) (GZ-SELECTIVE GTPASE-ACTIVATING PROTEIN) (G(Z)GAP). [SWISSPROT;Acc:O76081] 0.018683 0.158415086 RGS20
2934 RAP1 GTPASE-ACTIVATING PROTEIN 1 (RAP1GAP). [SWISSPROT;Acc:P47736] RAP1GAP
2935 CHROMOSOME 3P21.1 GENE SEQUENCE. [RefSeq;Acc:NM_013286] RBM15B
0.11804 2713 LAMIN B RECEPTOR (INTEGRAL NUCLEAR ENVELOPE INNER MEMBRANE PROTEIN) (LMN2R). [SWISSPROT;Acc:Q14739] 0.0244747 0.207342426 LBR
0.118068 2417 TUMOR DIFFERENTIALLY EXPRESSED 1 PROTEIN LIKE. [SWISSPROT;Acc:Q9NRX5] 0.0257797 0.218346207 SERINC1
0.118126 1850 "TRIACYLGLYCEROL LIPASE, GASTRIC PRECURSOR (EC 3.1.1.3) (GASTRIC LIPASE) (GL). [SWISSPROT;Acc:P07098]" 0.0275767 0.233451569 LIPF
1851 LYSOSOMAL ACID LIPASE/CHOLESTERYL ESTER HYDROLASE PRECURSOR (EC 3.1.1.13) (LAL) (ACID CHOLESTERYL ESTER HYDROLASE) (STEROL ESTERASE) (LIPASE A) (CHOLESTERYL ESTERASE). [SWISSPROT;Acc:P38571] LIPA
0.118439 1891 STROMAL CELL-DERIVED FACTOR 2 PRECURSOR (SDF-2). [SWISSPROT;Acc:Q99470] 0.0275634 0.23272233 SDF2
1892 THYMIDYLATE SYNTHASE (EC 2.1.1.45) (TS) (TSASE). [SWISSPROT;Acc:P04818] TYMS
0.118668 811 BRAIN PROTEIN 16. [RefSeq;Acc:NM_016458] 0.0310375 0.261549028 no value
0.118824 2077 PREFOLDIN SUBUNIT 6 (PROTEIN KE2). [SWISSPROT;Acc:O15212] 0.027225 0.22912038
0.118856 807 MELANOMA ANTIGEN P15 (MELANOMA-ASSOCIATED ANTIGEN RECOGNIZED BY T LYMPHOCYTES). [SWISSPROT;Acc:Q13084] 0.0311416 0.262011173 MRPL28
0.118935 2006 "HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC 1 (EC 2.1.1.43) (HISTONE H3-K9 METHYLTRANSFERASE 1) (H3-K9-HMTASE 1) (SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 1) (SU(VAR)3-9 HOMOLOG 1). [SWISSPROT;Acc:O43463]" 0.027437 0.230689032 SUV39H1
0.119125 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] 0.0249248 0.209232319 CHL1
0.119307 2601 YL-1 PROTEIN (TRANSCRIPTION FACTOR-LIKE 1). [SWISSPROT;Acc:Q15906] 0.0253936 0.212842499 VPS72
0.119364 2620 ESTERASE D (EC 3.1.1.1). [SWISSPROT;Acc:P10768] 0.025126 0.210498978 ESD
0.119396 798 0.0312832 0.262012128 TMCC3
0.119758 103 "SELENIDE,WATER DIKINASE 2 (EC 2.7.9.3) (SELENOPHOSPHATE SYNTHETASE 2) (SELENIUM DONOR PROTEIN 2). [SWISSPROT;Acc:Q99611]" 0.0447647 0.373792983 SEPHS2
0.119935 720 ZINC FINGER PROTEIN 258. [RefSeq;Acc:NM_145310] 0.0317441 0.264677534 ZMYM6
0.120084 2673 0.0251255 0.209232704 NFASC
0.120086 2590 DC11 PROTEIN. [RefSeq;Acc:NM_020186] 0.0255653 0.212891594 no value
2591 MELANOMA ANTIGEN RECOGNIZED BY T CELLS 2. [RefSeq;Acc:NM_018194] HHAT
2592 HEPATITIS C VIRUS CORE-BINDING PROTEIN 6; CERVICAL CANCER ONCOGENE 3. [RefSeq;Acc:NM_023934] no value
2593 "CALCIUM-BINDING MITOCHONDRIAL CARRIER PROTEIN ARALAR1 (SOLUTE CARRIER FAMILY 25, MEMBER 12). [SWISSPROT;Acc:O75746]" 0.0255652 0.212890762 SLC25A12
0.120157 749 ERYTHROID DIFFERENTIATION AND DENUCLEATION FACTOR 1. [SWISSPROT;Acc:O60584] 0.0317812 0.264497283 SLMO1
0.120229 2270 PUROMYCIN-SENSITIVE AMINOPEPTIDASE (EC 3.4.11.-) (PSA). [SWISSPROT;Acc:P55786] 0.0267797 0.222739106 NPEPPS
0.120439 2531 KERATIN ASSOCIATED PROTEIN 1-3; KERATIN ASSOCIATED PROTEIN 1.3. [RefSeq;Acc:NM_030966] 0.0258656 0.214760999 no value
0.120464 1114 POTENTIAL CARBOXYPEPTIDASE-LIKE PROTEIN X2 PRECURSOR. [SWISSPROT;Acc:Q8N436] 0.0302145 0.250817672 CPXM2

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/