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