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

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/