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

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/