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 Rank Hugo description expected final
Results: HTML CSV LaTeX Showing element 2508 to 2557 of 3206 in total
measured
Rank
Hugo
description
expected
final
0.293028 157 NCBP2L DJ820B18.1 (SIMILAR TO NUCLEAR CAP BINDING PROTEIN) (FRAGMENT). [SPTREMBL;Acc:Q8WWK2] 0.834941 0.350956535
0.293391 1047 SEPSECS SOLUBLE LIVER ANTIGEN/LIVER PANCREAS ANTIGEN. [RefSeq;Acc:NM_153825] 1.16068 0.252775097
0.293395 1848 SARS SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS). [SWISSPROT;Acc:P49591] 1.25677 0.233451626
0.29348 1158 AP2B1 ADAPTER-RELATED PROTEIN COMPLEX 2 BETA 1 SUBUNIT (BETA-ADAPTIN) (PLASMA MEMBRANE ADAPTOR HA2/AP2 ADAPTIN BETA SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 BETA LARGE CHAIN) (AP105B). [SWISSPROT;Acc:P21851] 1.17572 0.249617256
0.294007 2275 no value 1.32025 0.2226904
0.294256 2369 PDSS1 TRANS-PRENYLTRANSFERASE; POLYPRENYL PYROPHOSPHATE SYNTHETASE. [RefSeq;Acc:NM_014317] 1.3369 0.220103224
0.294647 1061 no value PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR-2 (HOMEOBOX PROTEIN PBX2) (G17 PROTEIN). [SWISSPROT;Acc:P40425] 1.16629 0.252636137
0.297365 161 MOBKL3 PREIMPLANTATION PROTEIN 3; LIKELY ORTHOLOG OF PREIMPLANTATION PROTEIN 3. [RefSeq;Acc:NM_015387] 0.860216 0.345686432
0.297474 2004 MTO1 MTO1 PROTEIN HOMOLOG (CGI-02). [SWISSPROT;Acc:Q9Y2Z2] 1.2892 0.230743096
0.298042 1610 TMEM189 UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 1 ISOFORM B; DNA-BINDING PROTEIN. [RefSeq;Acc:NM_003349] 1.24282 0.239811075
0.298587 2228 XYLB XYLULOKINASE HOMOLOG; XYLULOKINASE (H. INFLUENZAE) HOMOLOG. [RefSeq;Acc:NM_005108] 1.33096 0.224339574
0.299286 2165 no value 1.31793 0.227087933
0.299424 2931 GNAO1 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(O), ALPHA SUBUNIT 1. [SWISSPROT;Acc:P09471]" 1.89012 0.158415339
0.299475 2076 PFDN5 PREFOLDIN SUBUNIT 5 (C-MYC BINDING PROTEIN MM-1) (MYC MODULATOR 1). [SWISSPROT;Acc:Q99471] 1.30706 0.229121081
0.299765 1759 ATP6V1B1 "VACUOLAR ATP SYNTHASE SUBUNIT B, KIDNEY ISOFORM (EC 3.6.3.14) (V- ATPASE B1 SUBUNIT) (VACUOLAR PROTON PUMP B ISOFORM 1) (ENDOMEMBRANE PROTON PUMP 58 KDA SUBUNIT). [SWISSPROT;Acc:P15313]" 1.26636 0.236713889
0.301322 1069 PBX1 PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR-1 (HOMEOBOX PROTEIN PBX1) (HOMEOBOX PROTEIN PRL). [SWISSPROT;Acc:P40424] 1.19272 0.252634315
0.301597 2391 ATP5D "ATP SYNTHASE DELTA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P30049]" 1.37291 0.219677182
0.302351 753 SSB LUPUS LA PROTEIN (SJOGREN SYNDROME TYPE B ANTIGEN) (SS-B) (LA RIBONUCLEOPROTEIN) (LA AUTOANTIGEN). [SWISSPROT;Acc:P05455] 1.14316 0.264487036
0.303187 927 SMAD4 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 4 (SMAD 4) (MOTHERS AGAINST DPP HOMOLOG 4) (DELETION TARGET IN PANCREATIC CARCINOMA 4) (HSMAD4). [SWISSPROT;Acc:Q13485] 1.17661 0.257678415
0.303311 1401 DCX DOUBLECORTIN (LISSENCEPHALIN-X) (LIS-X) (DOUBLIN). [SWISSPROT;Acc:O43602] 1.24261 0.244091871
0.303744 2755 SSU72 1.49161 0.203634998
0.304036 335 MYC MYC PROTO-ONCOGENE PROTEIN (C-MYC). [SWISSPROT;Acc:P01106] 1.06655 0.285064929
0.304091 996 TLE2 TRANSDUCIN-LIKE ENHANCER PROTEIN 2 (ESG2). [SWISSPROT;Acc:Q04725] 1.19246 0.255011489
0.304267 1291 ARD1A N-TERMINAL ACETYLTRANSFERASE COMPLEX ARD1 SUBUNIT HOMOLOG (EC 2.3.1.-). [SWISSPROT;Acc:P41227] 1.23733 0.245906104
0.304269 2921 no value PNAS-18. [SPTREMBL;Acc:Q9BZU3] 1.80704 0.168379781
0.30514 2575 SLC5A5 SODIUM/IODIDE COTRANSPORTER (NA(+)/I(-) COTRANSPORTER) (SODIUM-IODIDE SYMPORTER) (NA+/I-SYMPORTER). [SWISSPROT;Acc:Q92911] 1.43033 0.213335384
0.305347 1970 RPS9 40S RIBOSOMAL PROTEIN S9. [SWISSPROT;Acc:P46781] 1.32095 0.231157122
0.305359 467 SARM1 "STERILE ALPHA AND TIR MOTIF CONTAINING 1; STERILE ALPHA AND HEAT/ARMADILLO MOTIF PROTEIN, ORTHOLOG OF DROSOPHILA. [RefSeq;Acc:NM_015077]" 1.11055 0.274961956
0.3063 2225 HAO2 "HYDROXYACID OXIDASE 2 (EC 1.1.3.15) (HAOX2) ((S)-2-HYDROXY-ACID OXIDASE, PEROXISOMAL) (LONG CHAIN ALPHA-HYDROXY ACID OXIDASE) (LONG- CHAIN L-2-HYDROXY ACID OXIDASE). [SWISSPROT;Acc:Q9NYQ3]" 1.36407 0.224548594
0.306804 1442 TBL3 TRANSDUCIN BETA-LIKE 3; WD-REPEAT PROTEIN SAZD. [RefSeq;Acc:NM_006453] 1.26013 0.243470118
0.306813 145 PDXDC1 SIMILAR TO EXPRESSED SEQUENCE AA415817. [SPTREMBL;Acc:Q8N4Q9] 0.87318 0.351374287
0.307072 1237 SMARCA5 SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN A5; SUCROSE NONFERMENTING-LIKE 5. [RefSeq;Acc:NM_003601] 1.2397 0.247698637
0.307359 599 ZIC2 ZINC FINGER PROTEIN ZIC 2 (ZINC FINGER PROTEIN OF THE CEREBELLUM 2). [SWISSPROT;Acc:O95409] 1.14212 0.269112703
0.30758 2166 no value 60S RIBOSOMAL PROTEIN L7. [SWISSPROT;Acc:P18124] 1.35464 0.227056635
0.307623 1240 KCND3 "POTASSIUM VOLTAGE-GATED CHANNEL, SHAL-RELATED SUBFAMILY, MEMBER 3 ISOFORM 1; SHA1-RELATED POTASSIUM CHANNEL KV4.3; VOLTAGE-GATED K+ CHANNEL; POTASSIUM IONIC CHANNEL KV4.3; VOLTAGE-GATED POTASSIUM CHANNEL KV4.3. [RefSeq;Acc:NM_004980]" 1.24236 0.247611803
0.308685 956 RPL24 60S RIBOSOMAL PROTEIN L24 (L30). [SWISSPROT;Acc:P38663] 1.20423 0.256333923
0.308754 2045 LSM4 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM4 (GLYCINE-RICH PROTEIN) (GRP). [SWISSPROT;Acc:Q9Y4Z0] 1.34189 0.230088904
0.309779 495 R3HDM1 R3H DOMAIN PROTEIN 1. [SWISSPROT;Acc:Q15032] 1.12934 0.274300919
0.309836 528 PPP1R12B "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 12B ISOFORM A; MYOSIN PHOSPHATASE REGULATORY SUBUNIT; MYOSIN PHOSPHATASE, TARGET SUBUNIT 2. [RefSeq;Acc:NM_002481]" 1.13987 0.271816962
0.310048 295 EFHC2 1.02794 0.301620717
0.310118 19 ANKS1B E2A-PBX1-ASSOCIATED PROTEIN; PUTATIVE 47 KDA PROTEIN. [RefSeq;Acc:NM_020140] 0.652691 0.475137546
0.310225 2947 PFKL "6-PHOSPHOFRUCTOKINASE, LIVER TYPE (EC 2.7.1.11) (PHOSPHOFRUCTOKINASE 1) (PHOSPHOHEXOKINASE) (PHOSPHOFRUCTO-1-KINASE ISOZYME B) (PFK-B). [SWISSPROT;Acc:P17858]" 2.04623 0.151608079
0.310615 3108 CDK2AP1 CYCLIN-DEPENDENT KINASE 2-ASSOCIATED PROTEIN 1 (CDK2-ASSOCIATED PROTEIN 1) (PUTATIVE ORAL CANCER SUPPRESSOR) (DELETED IN ORAL CANCER- 1) (DOC-1). [SWISSPROT;Acc:O14519] 3.36807 0.09222344
0.310662 1046 HSP90AA2 HEAT SHOCK PROTEIN HSP 90-ALPHA (HSP 86). [SWISSPROT;Acc:P07900] 1.22676 0.253237797
0.310673 1258 KIF23 KINESIN-LIKE PROTEIN KIF23 (MITOTIC KINESIN-LIKE PROTEIN-1) (KINESIN- LIKE PROTEIN 5). [SWISSPROT;Acc:Q02241] 1.25609 0.247333392
0.31086 1836 LSM1 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM1 (SMALL NUCLEAR RIBONUCLEAR CASM) (CANCER-ASSOCIATED SM-LIKE). [SWISSPROT;Acc:O15116] 1.32969 0.233783814
0.310893 1322 no value 60S ACIDIC RIBOSOMAL PROTEIN P1. [SWISSPROT;Acc:P05386] 1.26602 0.245567211
0.311095 2017 SDHB "SUCCINATE DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN, MITOCHONDRIAL PRECURSOR (EC 1.3.5.1) (IP) (IRON-SULFUR SUBUNIT OF COMPLEX II). [SWISSPROT;Acc:P21912]" 1.34923 0.230572252
0.311796 1413 PIH1D1 1.27783 0.244004289
0.311829 1485 VAC14 1.28408 0.242842346

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/