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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measured Gene expected Hugo final description Rank
Results: HTML CSV LaTeX Showing element 451 to 500 of 3206 in total
measured
expected
Hugo
final
description
Rank
0.0359748 0.135679 RCOR3 0.265146412 708
0.0359807 0.132771 TBC1D22B 0.270998185 TBC1 DOMAIN FAMILY PROTEIN C22ORF4-LIKE (FRAGMENT). [SWISSPROT;Acc:Q9NU19] 559
0.0360136 0.15771 COX4I1 0.228353307 "CYTOCHROME C OXIDASE SUBUNIT IV ISOFORM 1, MITOCHONDRIAL PRECURSOR (EC 1.9.3.1) (COX IV-1) (CYTOCHROME C OXIDASE POLYPEPTIDE IV). [SWISSPROT;Acc:P13073]" 2101
COX4I2 "CYTOCHROME C OXIDASE SUBUNIT IV ISOFORM 2, MITOCHONDRIAL PRECURSOR (EC 1.9.3.1) (COX IV-2). [SWISSPROT;Acc:Q96KJ9]" 2099
PPIB PEPTIDYL-PROLYL CIS-TRANS ISOMERASE B PRECURSOR (EC 5.2.1.8) (PPIASE) (ROTAMASE) (CYCLOPHILIN B) (S-CYCLOPHILIN) (SCYLP) (CYP-S1). [SWISSPROT;Acc:P23284] 2100
0.0360283 0.136657 RAB11FIP1 0.263640355 RAB COUPLING PROTEIN; RAB-INTERACTING RECYCLING PROTEIN; RAB EFFECTOR PROTEIN; RAB11-FAMILY INTERACTING PROTEIN 1. [RefSeq;Acc:NM_025151] 763
0.036083 0.155117 MAP4 0.232617959 MICROTUBULE-ASSOCIATED PROTEIN 4 (MAP 4). [SWISSPROT;Acc:P27816] 1895
0.036112 0.141665 B3GNT1 0.254911234 "N-ACETYLLACTOSAMINIDE BETA-1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE (EC 2.4.1.149) (POLY-N-ACETYLLACTOSAMINE EXTENSION ENZYME) (I-BETA- 1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE) (IGNT) (UDP-GLCNAC:BETAGAL BETA- 1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE 6). [SWISSP" 999
0.0361228 0.153963 COG7 0.234620006 CONSERVED OLIGOMERIC GOLGI COMPLEX COMPONENT 7. [SWISSPROT;Acc:P83436] 1804
0.0362497 0.133763 C20orf118 0.270999454 DJ132F21.2 (CONTAINS A NOVEL PROTEIN SIMILAR TO THE L82E FROM DROSOPHILA) (FRAGMENT). [SPTREMBL;Acc:Q9H125] 555
0.0362539 0.158511 ARHGEF4 0.228715357 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 4 ISOFORM A; APC-STIMULATED GUANINE NUCLEOTIDE EXCHANGE FACTOR. [RefSeq;Acc:NM_015320] 2091
0.0364961 0.150941 no value 0.241790501 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 7 (ADP-RIBOSYLATION FACTOR-LIKE PROTEIN LAK). [SWISSPROT;Acc:P56559] 1550
0.0365106 0.167562 RECQL5 0.217893078 ATP-DEPENDENT DNA HELICASE Q5 (RECQ PROTEIN-LIKE 5) (RECQ5). [SWISSPROT;Acc:O94762] 2424
0.0365299 0.353982 C1orf156 0.103197055 3070
0.0365656 0.307503 DYNLT3 0.11891136 T-COMPLEX ASSOCIATED-TESTIS-EXPRESSED 1-LIKE (PROTEIN 91/23). [SWISSPROT;Acc:P51808] 3027
0.0365698 0.138711 C14orf122 0.26364023 PROTEIN C14ORF122 (CGI-112). [SWISSPROT;Acc:Q9Y3B6] 766
0.0366052 0.143236 PERLD1 0.255558658 CAB2. [RefSeq;Acc:NM_033419] 970
0.0366237 0.174446 SCAMP2 0.209942905 SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 2. [SWISSPROT;Acc:O15127] 2655
0.0366305 0.166118 TXNDC1 0.220508915 THIOREDOXIN DOMAIN CONTAINING; THIOREDOXIN-RELATED TRANSMEMBRANE PROTEIN; THIOREDOXIN DOMAIN-CONTAINING. [RefSeq;Acc:NM_030755] 2346
0.0366317 0.148106 AURKA 0.247334342 SERINE/THREONINE KINASE 6 (EC 2.7.1.37) (SERINE/THREONINE KINASE 15) (AURORA/IPL1-RELATED KINASE 1) (AURORA-RELATED KINASE 1) (HARK1) (AURORA-A) (BREAST-TUMOR-AMPLIFIED KINASE). [SWISSPROT;Acc:O14965] 1255
CYLD "CYLINDROMATOSIS (TURBAN TUMOR SYNDROME); CYLINDROMATOSIS 1, TURBAN TUMOR SYNDROME. [RefSeq;Acc:NM_015247]" 1256
0.0366899 0.271591 STT3B 0.135092474 SOURCE OF IMMUNODOMINANT MHC-ASSOCIATED PEPTIDES; HOMOLOG OF YEAST STT3 GENE. [RefSeq;Acc:NM_178862] 2998
0.036734 0.190263 PTPRB 0.193069593 PROTEIN-TYROSINE PHOSPHATASE BETA PRECURSOR (EC 3.1.3.48) (R-PTP- BETA). [SWISSPROT;Acc:P23467] 2833
0.0367538 0.139602 no value 0.263275598 "SIRTUIN 7; SIR2-RELATED PROTEIN TYPE 7; SIRTUIN TYPE 7; SIRTUIN (SILENT MATING TYPE INFORMATION REGULATION 2, S.CEREVISIAE, HOMOLOG) 7; SILENT MATING TYPE INFORMATION REGULATION 2, S.CEREVISIAE, HOMOLOG 7; SIRTUIN SILENT MATING TYPE INFORMATION REGULATION" 773
0.0368025 0.204515 DPP9 0.179950126 DIPEPTIDYLPEPTIDASE 9; DIPEPTIDYL PEPTIDASE 9; DIPEPTIDYL PEPTIDASE IV-RELATED PROTEIN-2. [RefSeq;Acc:NM_139159] 2887
0.0368198 0.14147 TLX2 0.260265781 T-CELL LEUKEMIA HOMEOBOX PROTEIN 2 (HOMEOBOX PROTEIN HOX-11L1) (NEURAL CREST HOMEOBOX PROTEIN). [SWISSPROT;Acc:O43763] 870
0.036822 0.15167 no value 0.242777082 IMPORTIN 7; RAN-BINDING PROTEIN 7. [RefSeq;Acc:NM_006391] 1495
ARFGEF2 BREFELDIN A-INHIBITED GUANINE NUCLEOTIDE-EXCHANGE PROTEIN 2 (BREFELDIN A-INHIBITED GEP 2). [SWISSPROT;Acc:Q9Y6D5] 1496
0.0368814 0.136094 no value 0.270999456 SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH-LIKE PROTEIN 2 (FOVEA-ASSOCIATED SH3 DOMAIN BINDING PROTEIN). [SWISSPROT;Acc:Q9UJC5] 554
0.0368889 0.145611 CSDE1 0.25333869 UNR PROTEIN. [SWISSPROT;Acc:O75534] 1036
0.0369154 0.147123 MTR 0.250915221 "5-METHYLTETRAHYDROFOLATE--HOMOCYSTEINE METHYLTRANSFERASE (EC 2.1.1.13) (METHIONINE SYNTHASE, VITAMIN-B12 DEPENDENT) (MS). [SWISSPROT;Acc:Q99707]" 1107
0.0369504 0.140933 GPATCH1 0.262184158 EVOLUTIONARILY CONSERVED G-PATCH DOMAIN CONTAINING. [RefSeq;Acc:NM_018025] 788
0.0370125 0.107534 MSI2 0.344193464 MUSASHI 2 ISOFORM A. [RefSeq;Acc:NM_138962] 164
0.0370257 0.132897 TSR2 0.278604483 396
0.0370628 0.160934 SIN3B 0.230298135 2027
0.0370737 0.147075 ZFAND1 0.252073432 1081
0.0370824 0.136931 GALNTL1 0.270810846 SIMILAR TO EXPRESSED SEQUENCE AI415388 (FRAGMENT). [SPTREMBL;Acc:Q8N428] 564
0.0371202 0.141681 ZMYND8 0.261998433 PROTEIN KINASE C BINDING PROTEIN 1 (RACK7) (CUTANEOUS T-CELL LYMPHOMA ASSOCIATED ANTIGEN SE14-3) (CTCL TUMOR ANTIGEN SE14-3) (ZINC FINGER MYND DOMAIN CONTAINING PROTEIN 8). [SWISSPROT;Acc:Q9ULU4] 809
0.0371369 0.196598 no value 0.188897649 2872
0.0371738 0.137173 SH3BGRL 0.270999395 SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH-LIKE PROTEIN. [SWISSPROT;Acc:O75368] 556
0.0372023 0.196899 no value 0.188941031 CGI-142; HEPATOMA-DERIVED GROWTH FACTOR 2. [RefSeq;Acc:NM_016073] 2862
ORAI3 2863
PARK2 "PARKINSON DISEASE (AUTOSOMAL RECESSIVE, JUVENILE) 2, PARKIN ISOFORM 1; PARKIN. [RefSeq;Acc:NM_004562]" 2864
TMEM131 RW1 PROTEIN (FRAGMENT). [SWISSPROT;Acc:Q92545] 2861
0.03729 0.156155 C10orf83 0.238801191 44050 PROTEIN. [RefSeq;Acc:NM_178832] 1666
0.0373117 0.130845 no value 0.28515954 GA BINDING PROTEIN BETA-2 CHAIN (GABP-BETA-2 SUBUNIT) (TRANSCRIPTION FACTOR E4TF1-47) (GAPBP-2) (NUCLEAR RESPIRATORY FACTOR-2 SUBUNIT GAMMA). [SWISSPROT;Acc:Q06545] 333
0.0373336 0.147992 JUP 0.25226769 JUNCTION PLAKOGLOBIN (DESMOPLAKIN III). [SWISSPROT;Acc:P14923] 1074
0.0373888 0.123882 PMP2 0.301809787 MYELIN P2 PROTEIN. [SWISSPROT;Acc:P02689] 288
0.0374306 0.143817 TLX1 0.260265476 T-CELL LEUKEMIA HOMEOBOX PROTEIN 1 (HOMEOBOX PROTEIN HOX-11) (TCL-3 PROTO-ONCOGENE). [SWISSPROT;Acc:P31314] 873
0.0374428 0.198705 CTNNAL1 0.188434111 "CATENIN (CADHERIN-ASSOCIATED PROTEIN), ALPHA-LIKE 1; ALPHA-CATULIN. [RefSeq;Acc:NM_003798]" 2875

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/