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 Gene measured Rank final description Hugo
Results: HTML CSV LaTeX Showing element 152 to 201 of 3206 in total
expected
measured
Rank
final
description
Hugo
0.115356 0.0279589 1516 0.242370575 DNA REPLICATION LICENSING FACTOR MCM3 (DNA POLYMERASE ALPHA HOLOENZYME-ASSOCIATED PROTEIN P1) (RLF BETA SUBUNIT) (P102 PROTEIN) (P1-MCM3). [SWISSPROT;Acc:P25205] MCM3
0.11537 0.0275762 1647 0.23902401 no value
0.115399 0.0254221 2356 0.220297403 ZINC FINGER PROTEIN GLI1 (GLIOMA-ASSOCIATED ONCOGENE) (ONCOGENE GLI). [SWISSPROT;Acc:P08151] GLI1
2357 ZINC FINGER PROTEIN GLI2 (TAX HELPER PROTEIN). [SWISSPROT;Acc:P10070] GLI2
0.115441 0.0252512 2405 0.218736844 INTEGRAL MEMBRANE PROTEIN 2A (E25 PROTEIN). [SWISSPROT;Acc:O43736] ITM2A
0.115449 0.0285544 1257 0.247333455 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] AURKB
0.116194 0.0249538 2535 0.214759798 "KERATIN, ULTRA HIGH-SULFUR MATRIX PROTEIN B (UHS KERATIN B) (UHS KERB). [SWISSPROT;Acc:O75690]" KRTAP5-8
0.116238 0.0303497 830 0.26109964 KETOHEXOKINASE (EC 2.7.1.3) (HEPATIC FRUCTOKINASE). [SWISSPROT;Acc:P50053] KHK
0.116288 0.0249741 2532 0.214760766 KERATIN ASSOCIATED PROTEIN 1.5. [RefSeq;Acc:NM_031957] no value
0.116515 0.0305282 808 0.2620109 TMCC1
0.116699 0.0355659 276 0.304766108 ENTEROPEPTIDASE PRECURSOR (EC 3.4.21.9) (ENTEROKINASE). [SWISSPROT;Acc:P98073] PRSS7
0.116854 0.0250957 2530 0.214761155 "KERATIN, ULTRA HIGH-SULFUR MATRIX PROTEIN A (UHS KERATIN A) (UHS KERA). [SWISSPROT;Acc:P26371]" no value
0.116875 0.030934 730 0.264675936 ZINC FINGER PROTEIN 261 (DXS6673E PROTEIN). [SWISSPROT;Acc:Q14202] ZMYM3
0.117061 0.0256055 2406 0.218736385 INTEGRAL MEMBRANE PROTEIN 2C (TRANSMEMBRANE PROTEIN BRI3) (NPD018). [SWISSPROT;Acc:Q9NQX7] ITM2C
0.117481 0.0246707 2638 0.209997361 TRANSFORMING PROTEIN RHOA (H12). [SWISSPROT;Acc:P06749] RHOA
2639 3-MERCAPTOPYRUVATE SULFURTRANSFERASE (EC 2.8.1.2) (MST). [SWISSPROT;Acc:P25325] MPST
2640 AARSD1
0.117581 0.0274494 1854 0.233450983 no value
0.117689 0.0258973 2375 0.220048603 THIAMIN PYROPHOSPHOKINASE 1; MOUSE THIAMIN PYROPHOSPHOKINASE HOMOLOG; THIAMINE PYROPHOSPHOKINASE. [RefSeq;Acc:NM_022445]
0.117755 0.0311669 731 0.26467581 ZINC FINGER PROTEIN 198 (FUSED IN MYELOPROLIFERATIVE DISORDERS PROTEIN) (REARRANGED IN ATYPICAL MYELOPROLIFERATIVE DISORDER PROTEIN). [SWISSPROT;Acc:Q9UBW7] ZMYM2
0.117865 0.0275157 1855 0.233450982 PRESENILIN-LIKE PROTEIN 2 (EC 3.4.99.-) (SPPL2A PROTEIN). [SWISSPROT;Acc:Q8TCT8] no value
0.117937 0.018683 2933 0.158415086 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] 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 0.0244747 2713 0.207342426 LAMIN B RECEPTOR (INTEGRAL NUCLEAR ENVELOPE INNER MEMBRANE PROTEIN) (LMN2R). [SWISSPROT;Acc:Q14739] LBR
0.118068 0.0257797 2417 0.218346207 TUMOR DIFFERENTIALLY EXPRESSED 1 PROTEIN LIKE. [SWISSPROT;Acc:Q9NRX5] SERINC1
0.118126 0.0275767 1850 0.233451569 "TRIACYLGLYCEROL LIPASE, GASTRIC PRECURSOR (EC 3.1.1.3) (GASTRIC LIPASE) (GL). [SWISSPROT;Acc:P07098]" 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 0.0275634 1891 0.23272233 STROMAL CELL-DERIVED FACTOR 2 PRECURSOR (SDF-2). [SWISSPROT;Acc:Q99470] SDF2
1892 THYMIDYLATE SYNTHASE (EC 2.1.1.45) (TS) (TSASE). [SWISSPROT;Acc:P04818] TYMS
0.118668 0.0310375 811 0.261549028 BRAIN PROTEIN 16. [RefSeq;Acc:NM_016458] no value
0.118824 0.027225 2077 0.22912038 PREFOLDIN SUBUNIT 6 (PROTEIN KE2). [SWISSPROT;Acc:O15212]
0.118856 0.0311416 807 0.262011173 MELANOMA ANTIGEN P15 (MELANOMA-ASSOCIATED ANTIGEN RECOGNIZED BY T LYMPHOCYTES). [SWISSPROT;Acc:Q13084] MRPL28
0.118935 0.027437 2006 0.230689032 "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]" SUV39H1
0.119125 0.0249248 2674 0.209232319 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] CHL1
0.119307 0.0253936 2601 0.212842499 YL-1 PROTEIN (TRANSCRIPTION FACTOR-LIKE 1). [SWISSPROT;Acc:Q15906] VPS72
0.119364 0.025126 2620 0.210498978 ESTERASE D (EC 3.1.1.1). [SWISSPROT;Acc:P10768] ESD
0.119396 0.0312832 798 0.262012128 TMCC3
0.119758 0.0447647 103 0.373792983 "SELENIDE,WATER DIKINASE 2 (EC 2.7.9.3) (SELENOPHOSPHATE SYNTHETASE 2) (SELENIUM DONOR PROTEIN 2). [SWISSPROT;Acc:Q99611]" SEPHS2
0.119935 0.0317441 720 0.264677534 ZINC FINGER PROTEIN 258. [RefSeq;Acc:NM_145310] ZMYM6
0.120084 0.0251255 2673 0.209232704 NFASC
0.120086 0.0255652 2593 0.212890762 "CALCIUM-BINDING MITOCHONDRIAL CARRIER PROTEIN ARALAR1 (SOLUTE CARRIER FAMILY 25, MEMBER 12). [SWISSPROT;Acc:O75746]" SLC25A12
0.0255653 2590 0.212891594 DC11 PROTEIN. [RefSeq;Acc:NM_020186] 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
0.120157 0.0317812 749 0.264497283 ERYTHROID DIFFERENTIATION AND DENUCLEATION FACTOR 1. [SWISSPROT;Acc:O60584] SLMO1
0.120229 0.0267797 2270 0.222739106 PUROMYCIN-SENSITIVE AMINOPEPTIDASE (EC 3.4.11.-) (PSA). [SWISSPROT;Acc:P55786] NPEPPS
0.120439 0.0258656 2531 0.214760999 KERATIN ASSOCIATED PROTEIN 1-3; KERATIN ASSOCIATED PROTEIN 1.3. [RefSeq;Acc:NM_030966] no value
0.120464 0.0302145 1114 0.250817672 POTENTIAL CARBOXYPEPTIDASE-LIKE PROTEIN X2 PRECURSOR. [SWISSPROT;Acc:Q8N436] CPXM2
1115 POTENTIAL CARBOXYPEPTIDASE X PRECURSOR (EC 3.4.17.-) (METALLOCARBOXYPEPTIDASE CPX-1). [SWISSPROT;Acc:Q96SM3] CPXM1

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/