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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Gene Rank expected description measured Hugo final
Results: HTML CSV LaTeX Showing element 1701 to 1750 of 3206 in total
Rank
expected
description
measured
Hugo
final
1701 0.883788 NEMO-LIKE KINASE; LIKELY ORTHOLOG OF MOUSE NEMO LIKE KINASE. [RefSeq;Acc:NM_016231] 0.210207 NLK 0.237847764
1702 0.173407 ELKS PROTEIN. [RefSeq;Acc:NM_015064] 0.0412444 ERC1 0.237847376
1703 3.27908 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 3 (26S PROTEASOME REGULATORY SUBUNIT S3) (PROTEASOME SUBUNIT P58). [SWISSPROT;Acc:O43242] 0.779642 PSMD3 0.237762421
1704 0.241075 DJ408B20.3 (NOVEL PROTEIN SIMILAR TO 60S ACIDIC RIBOSOMAL PROTEIN P2 (RPLP2)). [SPTREMBL;Acc:Q9H5A9] 0.0573148 no value 0.237746759
1705 0.385556 BETA-CENTRACTIN (ACTIN-RELATED PROTEIN 1B) (ARP1B). [SWISSPROT;Acc:P42025] 0.0916612 ACTR1B 0.237737709
1706 0.407134 ALPHA-CENTRACTIN (CENTRACTIN) (CENTROSOME-ASSOCIATED ACTIN HOMOLOG) (ACTIN-RPV) (ARP1). [SWISSPROT;Acc:P42024] 0.0967911 ACTR1A 0.237737698
1707 3.57194 26S PROTEASE REGULATORY SUBUNIT 6B (MIP224) (MB67 INTERACTING PROTEIN) (TAT-BINDING PROTEIN-7) (TBP-7). [SWISSPROT;Acc:P43686] 0.848985 PSMC4 0.237681764
1708 0.66831 VESICLE-FUSING ATPASE (EC 3.6.4.6) (VESICULAR-FUSION PROTEIN NSF) (N- ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN) (NEM-SENSITIVE FUSION PROTEIN). [SWISSPROT;Acc:P46459] 0.15883 NSF 0.23765917
1709 3.92714 26S PROTEASE REGULATORY SUBUNIT 7 (MSS1 PROTEIN). [SWISSPROT;Acc:P35998] 0.933253 PSMC2 0.237641897
1710 3.49797 60S RIBOSOMAL PROTEIN L4 (L1). [SWISSPROT;Acc:P36578] 0.83123 RPL4 0.237632112
1711 0.768033 0.18248 PNPLA7 0.237593958
1712 2.81169 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 11 (26S PROTEASOME REGULATORY SUBUNIT S9) (26S PROTEASOME REGULATORY SUBUNIT P44.5). [SWISSPROT;Acc:O00231] 0.667497 PSMD11 0.237400638
1713 3.16322 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 6 (26S PROTEASOME REGULATORY SUBUNIT S10) (P42A) (PROTEASOME REGULATORY PARTICLE SUBUNIT P44S10). [SWISSPROT;Acc:Q15008] 0.750885 PSMD6 0.237379948
1714 0.382985 "NUCLEOLAR PROTEIN FAMILY A, MEMBER 2; COMPONENT OF THE H/ACA SNORNP. [RefSeq;Acc:NM_017838]" 0.0909039 NOLA2 0.237356293
1715 0.127662 "TRANSCRIPTION INITIATION FACTOR IIF, ALPHA SUBUNIT (TFIIF-ALPHA) (TRANSCRIPTION INITIATION FACTOR RAP74). [SWISSPROT;Acc:P35269]" 0.0303013 GTF2F1 0.237355674
1716 1.13756 VACUOLAR PROTON TRANSLOCATING ATPASE 116 KDA SUBUNIT A ISOFORM 1 (CLATHRIN-COATED VESICLE/SYNAPTIC VESICLE PROTON PUMP 116 KDA SUBUNIT) (VACUOLAR PROTON PUMP SUBUNIT 1) (VACUOLAR ADENOSINE TRIPHOSPHATASE SUBUNIT AC116). [SWISSPROT;Acc:Q93050] 0.269961 ATP6V0A1 0.237315834
1717 0.944489 "ATPASE, H+ TRANSPORTING, LYSOSOMAL V0 SUBUNIT A ISOFORM 4; VACUOLAR PROTON PUMP 116 KDA ACCESSORY SUBUNIT; VACUOLAR PROTON PUMP, SUBUNIT 2; H(+)-TRANSPORTING TWO-SECTOR ATPASE, NONCATALYTIC ACCESSORY PROTEIN 1B; ATPASE, H+ TRANSPORTING, LYSOSOMAL (VACUOLA" 0.224133 ATP6V0A4 0.237306099
1718 0.892673 VACUOLAR PROTON TRANSLOCATING ATPASE 116 KDA SUBUNIT A ISOFORM 2 (V-ATPASE 116-KDA ISOFORM A2) (TJ6). [SWISSPROT;Acc:Q9Y487] 0.211834 ATP6V0A2 0.237303021
1719 0.852079 VACUOLAR PROTON TRANSLOCATING ATPASE 116 KDA SUBUNIT A ISOFORM 3 (V- ATPASE 116-KDA ISOFORM A3) (OSTEOCLASTIC PROTON PUMP 116 KDA SUBUNIT) (OC-116 KDA) (OC116) (T-CELL IMMUNE REGULATOR 1) (T CELL IMMUNE RESPONSE CDNA7 PROTEIN) (TIRC7). [SWISSPROT;A 0.202198 TCIRG1 0.237299593
1720 1.35288 MIDASIN (MIDAS-CONTAINING PROTEIN). [SWISSPROT;Acc:Q9NU22] 0.321031 MDN1 0.237294512
1721 0.652697 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 9 (26S PROTEASOME REGULATORY SUBUNIT P27). [SWISSPROT;Acc:O00233] 0.154828 PSMD9 0.237212673
1722 1.54946 "PROBABLE DIMETHYLADENOSINE TRANSFERASE (EC 2.1.1.-) (S- ADENOSYLMETHIONINE-6-N',N'-ADENOSYL(RRNA) DIMETHYLTRANSFERASE) (18S RRNA DIMETHYLASE). [SWISSPROT;Acc:Q9UNQ2]" 0.367472 DIMT1L 0.237161334
1723 0.971531 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 45 (H-VPS45) (HLVPS45). [SWISSPROT;Acc:Q9NRW7] 0.230384 VPS45 0.237134996
1724 0.231086 0.0547796 RIOK2 0.237052872
1725 0.450769 0.10685 VPS25 0.23703937
1726 CHMP6
1727 0.0742417 "GLUTAMATE DECARBOXYLASE, 65 KDA ISOFORM (EC 4.1.1.15) (GAD-65) (65 KDA GLUTAMIC ACID DECARBOXYLASE). [SWISSPROT;Acc:Q05329]" 0.0175982 GAD2 0.237039292
1728 0.332307 0.0787698 C12orf26 0.237039244
1729 0.238547 "GAMMA-SOLUBLE NSF ATTACHMENT PROTEIN (SNAP-GAMMA) (N-ETHYLMALEIMIDE- SENSITIVE FACTOR ATTACHMENT PROTEIN, GAMMA). [SWISSPROT;Acc:Q99747]" 0.056545 NAPG 0.237039242
1730 0.0901539 NOSTRIN. [RefSeq;Acc:NM_052946] 0.02137 NOSTRIN 0.237039108
1731 no value
1732 0.0899059 "GLUTAMATE DECARBOXYLASE, 67 KDA ISOFORM (EC 4.1.1.15) (GAD-67) (67 KDA GLUTAMIC ACID DECARBOXYLASE). [SWISSPROT;Acc:Q99259]" 0.0213112 GAD1 0.237038949
1733 0.0703876 "LIV-1 PROTEIN, ESTROGEN REGULATED. [RefSeq;Acc:NM_012319]" 0.0166846 SLC39A6 0.23703891
1734 0.180308 EAP30 SUBUNIT OF ELL COMPLEX. [RefSeq;Acc:NM_007241] 0.04274 SNF8 0.237038845
1735 0.760447 RAD54-LIKE PROTEIN; RAD54 HOMOLOG. [RefSeq;Acc:NM_003579] 0.180241 RAD54L 0.237019805
1736 2.66198 0.630807 ATPBD3 0.236969098
1737 0.399107 GLUTAMINYL-TRNA SYNTHASE (GLUTAMINE-HYDROLYZING)-LIKE 1. [RefSeq;Acc:NM_018292] 0.094576 QRSL1 0.236969033
1738 0.399707 FATTY-ACID AMIDE HYDROLASE (EC 3.1.-.-) (OLEAMIDE HYDROLASE) (ANANDAMIDE AMIDOHYDROLASE). [SWISSPROT;Acc:O00519] 0.0947181 FAAH 0.23696883
1739 0.399507 "URACIL-DNA GLYCOSYLASE, MITOCHONDRIAL PRECURSOR (EC 3.2.2.-) (UDG). [SWISSPROT;Acc:P13051]" 0.0946707 UNG 0.236968814
1740 "PROBABLE GLUTAMYL-TRNA(GLN) AMIDOTRANSFERASE SUBUNIT B, MITOCHONDRIAL PRECURSOR (EC 6.3.5.-) (GLU-ADT SUBUNIT B) (CYTOCHROME OXIDASE ASSEMBLY FACTOR PET112 HOMOLOG). [SWISSPROT;Acc:O75879]" PET112L
1741 0.133236 COACTOSIN-LIKE PROTEIN. [SWISSPROT;Acc:Q14019] 0.0315727 COTL1 0.236968237
1742 0.2855 CONSERVED OLIGOMERIC GOLGI COMPLEX COMPONENT 6. [SWISSPROT;Acc:Q9Y2V7] 0.0676104 COG6 0.236814011
1743 0.968071 40S RIBOSOMAL PROTEIN S28. [SWISSPROT;Acc:P25112] 0.229236 no value 0.236796681
1744 1.51127 "VACUOLAR ATP SYNTHASE SUBUNIT B, BRAIN ISOFORM (EC 3.6.3.14) (V-ATPASE B2 SUBUNIT) (VACUOLAR PROTON PUMP B ISOFORM 2) (ENDOMEMBRANE PROTON PUMP 58 KDA SUBUNIT) (HO57). [SWISSPROT;Acc:P21281]" 0.357744 ATP6V1B2 0.236717463
1745 0.349234 GANGLIOSIDE-INDUCED DIFFERENTIATION-ASSOCIATED PROTEIN 1-LIKE 1. [RefSeq;Acc:NM_024034] 0.0826697 GDAP1L1 0.236717215
1746 0.566199 YEAST SEC31P HOMOLOG. [RefSeq;Acc:NM_014933] 0.134029 SEC31A 0.236717126
1747 2.02876 VACUOLAR ATP SYNTHASE SUBUNIT E (EC 3.6.3.14) (V-ATPASE E SUBUNIT) (VACUOLAR PROTON PUMP E SUBUNIT) (V-ATPASE 31 KDA SUBUNIT) (P31). [SWISSPROT;Acc:P36543] 0.480242 ATP6V1E1 0.236717009
1748 0.411298 GANGLIOSIDE-INDUCED DIFFERENTIATION-ASSOCIATED PROTEIN 1. [RefSeq;Acc:NM_018972] 0.0973611 GDAP1 0.236716687
1749 2.18869 VACUOLAR ATP SYNTHASE SUBUNIT D (EC 3.6.3.14) (V-ATPASE D SUBUNIT) (VACUOLAR PROTON PUMP D SUBUNIT) (V-ATPASE 28 KDA ACCESSORY PROTEIN). [SWISSPROT;Acc:Q9Y5K8] 0.518099 ATP6V1D 0.236716483
1750 0.237616 VACUOLAR ATP SYNTHASE SUBUNIT H (EC 3.6.3.14) (V-ATPASE H SUBUNIT) (VACUOLAR PROTON PUMP H SUBUNIT) (V-ATPASE 50/57 KDA SUBUNITS) (VACUOLAR PROTON PUMP SUBUNIT SFD) (CGI-11). [SWISSPROT;Acc:Q9UI12] 0.0562476 ATP6V1H 0.236716383

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/