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 measured Rank final description Hugo
Results: HTML CSV LaTeX Showing element 1052 to 1101 of 3206 in total
expected
measured
Rank
final
description
Hugo
0.315578 0.0869671 462 0.275580364 9 KDA PROTEIN. [SWISSPROT;Acc:P13994] CCDC130
463 65 KDA YES-ASSOCIATED PROTEIN (YAP65). [SWISSPROT;Acc:P46937] YAP1
464 MITOCHONDRIAL RIBOSOMAL PROTEIN L24. [RefSeq;Acc:NM_024540] MRPL24
465 E1A BINDING PROTEIN P400; P400 SWI2/SNF2-RELATED PROTEIN; CAGH32 PROTEIN; TRINUCLEOTIDE REPEAT CONTAINING 12. [RefSeq;Acc:NM_015409] EP400
0.315691 0.0608484 2841 0.192746705 AQUAPORIN-CD (AQP-CD) (WATER CHANNEL PROTEIN FOR RENAL COLLECTING DUCT) (ADH WATER CHANNEL) (AQUAPORIN 2) (COLLECTING DUCT WATER CHANNEL PROTEIN) (WCH-CD). [SWISSPROT;Acc:P41181] AQP2
0.315775 0.0764864 1531 0.242218035 ATP-DEPENDENT RNA HELICASE ROK1; ATP-DEPENDENT RNA HELICASE. [RefSeq;Acc:NM_007010] DDX52
0.315963 0.150125 21 0.475134747 NEURON NAVIGATOR 3; PORE MEMBRANE AND/OR FILAMENT INTERACTING LIKE PROTEIN 1; STEERIN 3. [RefSeq;Acc:NM_014903] NAV3
0.316634 0.0770791 1449 0.243432796 SALIVARY PROLINE-RICH PROTEIN PO (ALLELE K) [CONTAINS: PEPTIDE P-D] (FRAGMENT). [SWISSPROT;Acc:P10162] PRB4
0.316697 0.0610425 2840 0.192747326 LENS FIBER MAJOR INTRINSIC PROTEIN (MIP26) (MP26) (AQUAPORIN 0). [SWISSPROT;Acc:P30301] MIP
0.317178 0.0924045 318 0.291333258 COLORECTAL MUTANT CANCER PROTEIN (MCC PROTEIN). [SWISSPROT;Acc:P23508] MCC
0.317545 0.0736608 1921 0.231969642 FAD SYNTHETASE. [RefSeq;Acc:NM_025207] FLAD1
0.317655 0.0698995 2376 0.22004848 THIOREDOXIN-LIKE; PKC-INTERACTING COUSIN OF THIOREDOXIN. [RefSeq;Acc:NM_006541] GLRX3
0.318777 0.0884193 425 0.277370387 DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 47; HQP0256 PROTEIN. [RefSeq;Acc:NM_016355] no value
0.318821 0.0893365 363 0.280208957 SPLICING FACTOR 3B SUBUNIT 4 (SPLICEOSOME ASSOCIATED PROTEIN 49) (SAP 49) (SF3B50) (PRE-MRNA SPLICING FACTOR SF3B 49 KDA SUBUNIT). [SWISSPROT;Acc:Q15427] SF3B4
0.318867 0.0884444 421 0.277370816 UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 8 (EC 3.1.2.15) (UBIQUITIN THIOLESTERASE 8) (UBIQUITIN-SPECIFIC PROCESSING PROTEASE 8) (DEUBIQUITINATING ENZYME 8). [SWISSPROT;Acc:P40818] USP8
0.319234 0.0790456 1242 0.247610217 CYSTATHIONINE GAMMA-LYASE (EC 4.4.1.1) (GAMMA-CYSTATHIONASE). [SWISSPROT;Acc:P32929] CTH
0.319446 0.091005 338 0.28488383 METASTASIS-ASSOCIATED PROTEIN MTA1. [SWISSPROT;Acc:Q13330] MTA1
0.319772 0.0933039 316 0.291782583 SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN (SRP9). [SWISSPROT;Acc:P49458] SRP9
0.320798 0.0673673 2629 0.209999127 MAP KINASE-ACTIVATED PROTEIN KINASE 2 (EC 2.7.1.-) (MAPK-ACTIVATED PROTEIN KINASE 2) (MAPKAP KINASE 2) (MAPKAPK-2). [SWISSPROT;Acc:P49137] MAPKAPK2
0.321066 0.0837034 841 0.260704653 LEUCINE-RICH REPEAT PROTEIN LRRC3 PRECURSOR. [SWISSPROT;Acc:Q9BY71] LRRC3
0.32156 0.0769103 1637 0.239178691 ZINC FINGER PROTEIN 207. [SWISSPROT;Acc:O43670] ZNF207
0.322851 0.0777867 1573 0.240936841 BULLOUS PEMPHIGOID ANTIGEN 1 ISOFORMS 1/2/3/4/5/8 (230 KDA BULLOUS PEMPHIGOID ANTIGEN) (BPA) (HEMIDESMOSOMAL PLAQUE PROTEIN) (DYSTONIA MUSCULORUM PROTEIN) (FRAGMENT). [SWISSPROT;Acc:Q03001] DST
0.323185 0.0754524 1846 0.233465043 MCT-1 PROTEIN. [RefSeq;Acc:NM_014060] MCTS1
0.323402 0.0861152 674 0.26627912 KINESIN FAMILY MEMBER C3. [RefSeq;Acc:NM_005550] KIFC3
0.323509 0.0802494 1213 0.24805925 DYSTROPHIN. [SWISSPROT;Acc:P11532] no value
1214 ANGIOMOTIN. [RefSeq;Acc:NM_133265] AMOT
1215 "BETA-1-SYNTROPHIN (59 KDA DYSTROPHIN-ASSOCIATED PROTEIN A1, BASIC COMPONENT 1) (DAPA1B) (TAX INTERACTION PROTEIN 43) (TIP-43) (SYNTROPHIN 2) (BSYN2). [SWISSPROT;Acc:Q13884]" SNTB1
1216 NITRILASE 1. [RefSeq;Acc:NM_005600] NIT1
0.32416 0.0858635 714 0.264879998 MULTIPLE COAGULATION FACTOR DEFICIENCY 2; NEURAL STEM CELL DERIVED NEURONAL SURVIVAL PROTEIN; MULTIPLE COAGULATION FACTOR DEFICIENCY PROTEIN 2. [RefSeq;Acc:NM_139279] MCFD2
0.324189 0.090885 361 0.280345724 EXOCYST COMPLEX COMPONENT SEC8. [SWISSPROT;Acc:Q96A65] EXOC4
0.324228 0.0869771 626 0.268259065 no value
0.324347 0.0657247 2761 0.202636991 SAPS1
0.326253 0.0764303 1817 0.234266965 DNA FRAGMENTATION FACTOR ALPHA SUBUNIT (DNA FRAGMENTATION FACTOR 45 KDA SUBUNIT) (DFF-45) (INHIBITOR OF CAD) (ICAD). [SWISSPROT;Acc:O00273] DFFA
0.326494 0.0719255 2367 0.220296545 LIPOCALIN-INTERACTING MEMBRANE RECEPTOR. [RefSeq;Acc:NM_018113] LMBR1L
0.326785 0.0686246 2627 0.209999235 UDP-N-ACETYLGLUCOSAMINE--DOLICHYL-PHOSPHATE N- ACETYLGLUCOSAMINEPHOSPHOTRANSFERASE (EC 2.7.8.15) (GPT) (G1PT) (N-ACETYLGLUCOSAMINE-1-PHOSPHATE TRANSFERASE) (GLCNAC-1-P TRANSFERASE). [SWISSPROT;Acc:Q9H3H5] DPAGT1
0.326867 0.0765741 1819 0.234266842 ADAMTS-9 PRECURSOR (EC 3.4.24.-) (A DISINTEGRIN AND METALLOPROTEINASE WITH THROMBOSPONDIN MOTIFS 9) (ADAM-TS 9) (ADAM-TS9). [SWISSPROT;Acc:Q9P2N4] ADAMTS9
0.327175 0.132875 66 0.406128219 SYNAPSIN I (BRAIN PROTEIN 4.1). [SWISSPROT;Acc:P17600] SYN1
0.327271 0.0872849 671 0.266705269 INTERLEUKIN ENHANCER-BINDING FACTOR 1 (CELLULAR TRANSCRIPTION FACTOR ILF-1). [SWISSPROT;Acc:Q01167] FOXK2
0.327649 0.0789602 1570 0.240990206 LIM HOMEOBOX TRANSCRIPTION FACTOR 1 BETA (LIM/HOMEOBOX PROTEIN LMX1B) (LIM-HOMEOBOX PROTEIN 1.2) (LMX-1.2). [SWISSPROT;Acc:O60663] LMX1B
1571 LIM HOMEOBOX TRANSCRIPTION FACTOR 1 ALPHA (LIM/HOMEOBOX PROTEIN LMX1A) (LIM-HOMEOBOX PROTEIN 1.1) (LMX-1.1). [SWISSPROT;Acc:Q8TE12] LMX1A
0.327833 0.0766245 1837 0.233730283 C8orf53
0.32796 0.133193 79 0.406125747 SYNAPSIN III. [SWISSPROT;Acc:O14994] SYN3
0.328537 0.0869475 734 0.264650557 B-CELL LYMPHOMA 6 PROTEIN (BCL-6) (ZINC FINGER PROTEIN 51) (LAZ-3 PROTEIN) (BCL-5). [SWISSPROT;Acc:P41182] BCL6
735 ZINC FINGER PROTEIN SLUG (NEURAL CREST TRANSCRIPTION FACTOR SLUG) (SNAIL HOMOLOG 2). [SWISSPROT;Acc:O43623] SNAI2
736 PAS DOMAIN CONTAINING SERINE/THREONINE KINASE; PAS-SERINE/THREONINE KINASE. [RefSeq;Acc:NM_015148] PASK
0.330921 0.0849609 934 0.256740733 CYCLIN C. [SWISSPROT;Acc:P24863] CCNC
0.330932 0.0803487 1493 0.242795197 RECEPTOR PROTEIN-TYROSINE KINASE ERBB-2 PRECURSOR (EC 2.7.1.112) (P185ERBB2) (NEU PROTO-ONCOGENE) (C-ERBB-2) (TYROSINE KINASE-TYPE CELL SURFACE RECEPTOR HER2) (MLN 19). [SWISSPROT;Acc:P04626] ERBB2
0.331516 0.0693641 2671 0.209233039 "NUCLEAR FACTOR ERYTHROID 2 RELATED FACTOR 1 (NF-E2 RELATED FACTOR 1) (NFE2-RELATED FACTOR 1) (NUCLEAR FACTOR, ERYTHROID DERIVED 2, LIKE 1) (TRANSCRIPTION FACTOR 11) (TRANSCRIPTION FACTOR HBZ17) (TRANSCRIPTION FACTOR LCR-F1) (LOCUS CONTROL REGION-FACTOR 1)" NFE2L1
0.331704 0.0946713 328 0.285408979 PEROXIREDOXIN 4 (EC 1.11.1.-) (PRX-IV) (THIOREDOXIN PEROXIDASE AO372) (THIOREDOXIN-DEPENDENT PEROXIDE REDUCTASE A0372) (ANTIOXIDANT ENZYME AOE372) (AOE37-2). [SWISSPROT;Acc:Q13162] PRDX4
0.331879 0.0696821 2647 0.209962366 TUBBY RELATED PROTEIN 1 (TUBBY-LIKE PROTEIN 1). [SWISSPROT;Acc:O00294] TULP1

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/