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 [...,...].
Hugo Gene measured expected Rank final description
Results: HTML CSV LaTeX Showing element 101 to 150 of 3206 in total
Hugo  : no value
measured
expected
Rank
final
description
0.0506272 0.392576 3001 0.128961526 GABA-A RECEPTOR-ASSOCIATED PROTEIN. [SPTREMBL;Acc:Q9BY60]
0.0511645 0.124441 58 0.411154684 "DJ681N20.2 (NOVEL PROTEIN SIMILAR TO FERRITIN, LIGHT POLYPEPTIDE (FTL)). [SPTREMBL;Acc:Q9BYW6]"
0.0511995 0.238723 2553 0.214472422
0.0513128 0.278146 2881 0.184481531 ADAPTER-RELATED PROTEIN COMPLEX 3 BETA 2 SUBUNIT (BETA-ADAPTIN 3B) (AP-3 COMPLEX BETA-3B SUBUNIT) (BETA-3B-ADAPTIN) (NEURON-SPECIFIC VESICLE COAT PROTEIN BETA-NAP). [SWISSPROT;Acc:Q13367]
0.0533885 0.517345 3069 0.103197093
0.0544712 0.239562 2148 0.227378299 APOPTOSIS INHIBITOR FKSG2. [SWISSPROT;Acc:Q9HAU6]
0.0555455 0.180015 261 0.308560398 APOBEC-1 COMPLEMENTATION FACTOR ISOFORM 1; APOBEC-1 STIMULATING PROTEIN; APO-B RNA EDITING PROTEIN. [RefSeq;Acc:NM_014576]
0.0556846 0.180466 262 0.308560061
0.0560669 0.181705 263 0.308560029 RNA-BINDING PROTEIN. [RefSeq;Acc:NM_019027]
0.0561104 0.16661 180 0.336776904 TRINUCLEOTIDE REPEAT CONTAINING 15. [RefSeq;Acc:NM_015575]
0.0561617 0.26352 2582 0.213121205 BLOOD GROUP RH(CE) POLYPEPTIDE (RHESUS C/E ANTIGENS) (RH30A) (RHIXB) (RH POLYPEPTIDE 1) (RHPI). [SWISSPROT;Acc:P18577]
0.0564693 0.264963 2580 0.213121455
0.0568291 0.227574 1151 0.249717015 SPROUTY HOMOLOG 4 (SPRY-4). [SWISSPROT;Acc:Q9C004]
0.0568574 0.216002 777 0.263226266 HUNTINGTIN-ASSOCIATED PROTEIN-INTERACTING PROTEIN (DUO PROTEIN). [SWISSPROT;Acc:O60229]
0.0569865 0.250685 2151 0.227323135 STEROL REGULATORY ELEMENT BINDING PROTEIN-2 (SREBP-2) (STEROL REGULATORY ELEMENT-BINDING TRANSCRIPTION FACTOR 2). [SWISSPROT;Acc:Q12772]
0.0570468 0.282946 2768 0.20161727 ZINC FINGER PROTEIN 277. [SWISSPROT;Acc:Q9NRM2]
0.0571361 0.247068 1953 0.231256577 60S RIBOSOMAL PROTEIN L14 (CAG-ISL 7). [SWISSPROT;Acc:P50914]
0.0572133 0.287777 2799 0.198811232 "ATAXIN 2; OLIVOPONTOCEREBELLAR ATAXIA 2, AUTOSOMAL DOMINANT. [RefSeq;Acc:NM_002973]"
0.0573148 0.241075 1704 0.237746759 DJ408B20.3 (NOVEL PROTEIN SIMILAR TO 60S ACIDIC RIBOSOMAL PROTEIN P2 (RPLP2)). [SPTREMBL;Acc:Q9H5A9]
0.0577101 0.270506 2574 0.213341294
0.0580492 0.247338 1800 0.234695841
0.0588477 0.165745 127 0.355049624 ERO1-LIKE. [RefSeq;Acc:NM_014584]
0.0589414 0.254478 1940 0.231616878 "ISOLEUCYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.5) (ISOLEUCINE--TRNA LIGASE) (ILERS) (IRS). [SWISSPROT;Acc:P41252]"
0.0604093 0.274218 2366 0.220296625 PEPSIN A PRECURSOR (EC 3.4.23.1). [SWISSPROT;Acc:P00790]
0.0607427 0.257167 1764 0.236199435
0.0614814 0.240043 960 0.256126611 "ACYL-COA DEHYDROGENASE, SHORT/BRANCHED CHAIN SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 1.3.99.-) (SBCAD) (2-METHYL BRANCHED CHAIN ACYL-COA DEHYDROGENASE) (2-MEBCAD) (2-METHYLBUTYRYL-COENZYME A DEHYDROGENASE) (2-METHYLBUTYRYL-COA DEHYDROGENASE). [SWISSP"
0.061947 0.290115 2565 0.213525671 TETRATRICOPEPTIDE REPEAT PROTEIN 4 (MY044 PROTEIN). [SWISSPROT;Acc:O95801]
0.0637011 0.29203 2423 0.218132041 TRANSCRIPTION ELONGATION FACTOR A PROTEIN 1 (TRANSCRIPTION ELONGATION FACTOR S-II PROTEIN 1) (TRANSCRIPTION ELONGATION FACTOR TFIIS.O). [SWISSPROT;Acc:P23193]
0.0637349 0.231274 460 0.27558177699999997 COLLAGEN ALPHA 5(IV) CHAIN PRECURSOR. [SWISSPROT;Acc:P29400]
0.06383 0.157168 78 0.406125929 ASPARTATE BETA-HYDROXYLASE ISOFORM B; JUNCTIN ISOFORM 1; JUNCTATE; ASPARTYL/ASPARAGINYL-BETA-HYDROXYLASE; PEPTIDE-ASPARTATE BETA-DIOXYGENASE; HUMBUG. [RefSeq;Acc:NM_032468]
0.0640341 0.280704 2127 0.228119656 "GLYCINE DEHYDROGENASE [DECARBOXYLATING], MITOCHONDRIAL PRECURSOR (EC 1.4.4.2) (GLYCINE DECARBOXYLASE) (GLYCINE CLEAVAGE SYSTEM P- PROTEIN). [SWISSPROT;Acc:P23378]"
0.0646293 0.988493 3148 0.065381647 MELANOMA-ASSOCIATED ANTIGEN 3 (MAGE-3 ANTIGEN) (ANTIGEN MZ2-D). [SWISSPROT;Acc:P43357]
0.0648148 0.99133 3147 0.065381659 MELANOMA-ASSOCIATED ANTIGEN 1 (MAGE-1 ANTIGEN) (ANTIGEN MZ2-E). [SWISSPROT;Acc:P43355]
0.0651239 0.996058 3149 0.065381634 MELANOMA-ASSOCIATED ANTIGEN 4 (MAGE-4 ANTIGEN) (MAGE-X2) (MAGE-41). [SWISSPROT;Acc:P43358]
0.0651843 0.250194 852 0.260535025 KINESIN-LIKE PROTEIN KIF13B (KINESIN-LIKE PROTEIN GAKIN). [SWISSPROT;Acc:Q9NQT8]
0.0653411 0.271247 1584 0.240891512 HURPIN (HACAT UV-REPRESSIBLE SERPIN) (PROTEASE INHIBITOR 13) (HEADPIN) (SERPIN B13). [SWISSPROT;Acc:Q9UIV8]
0.0654179 0.277203 1772 0.235992756 HEAT SHOCK 70 KDA PROTEIN 1 (HSP70.1) (HSP70-1/HSP70-2). [SWISSPROT;Acc:P08107]
0.0669581 1.02411 3138 0.065381746 HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN HCA1. [RefSeq;Acc:NM_020932]
0.0671866 0.25292 688 0.265643682 SIGNAL-INDUCED PROLIFERATION-ASSOCIATED 1-LIKE 1. [RefSeq;Acc:NM_015556]
0.0678638 0.874459 3123 0.077606612 NUCLEAR DNA-BINDING PROTEIN; SMALL UNIQUE NUCLEAR RECEPTOR COREPRESSOR; C1D DNA-BINDING PROTEIN. [RefSeq;Acc:NM_006333]
0.0697761 0.263425 713 0.264880326 DJ153G14.2 (POSSIBLE CA BINDING PROTEIN SIMILAR TO NEFA) (FRAGMENT). [SPTREMBL;Acc:Q9UJN8]
0.0700456 0.287741 1448 0.243432809 BASIC PROLINE-RICH PEPTIDE P-E (IB-9). [SWISSPROT;Acc:P02811]
0.0733796 0.302004 1475 0.24297559 RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 (P21-RAC1) (RAS-LIKE PROTEIN TC25). [SWISSPROT;Acc:P15154]
0.0739754 0.28817 936 0.256707499 RHO INTERACTING PROTEIN 3. [RefSeq;Acc:NM_015134]
0.0746316 0.510598 2960 0.146165085 RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR-LIKE 2 (RALGDS-LIKE FACTOR) (RAS-ASSOCIATED PROTEIN RAB2L). [SWISSPROT;Acc:O15211]
0.0753031 0.176719 28 0.426117735 DOK-LIKE PROTEIN. [RefSeq;Acc:NM_024872]
0.0753661 0.312352 1557 0.241285793
0.0760628 0.309407 1298 0.245834128
0.079717 0.314025 1015 0.253855585 INTERSECTIN 2 (SH3 DOMAIN-CONTAINING PROTEIN 1B) (SH3P18) (SH3P18-LIKE WASP ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q9NZM3]
0.0798317 0.381544 2670 0.209233273 TRANSCRIPTION FACTOR MAFG (V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG G) (HMAF). [SWISSPROT;Acc:O15525]

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/