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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Rank measured Gene Hugo description expected final
Results: HTML CSV LaTeX Showing element 1708 to 1757 of 3206 in total
Rank
measured
Hugo
description
expected
final
1708 0.15883 NSF VESICLE-FUSING ATPASE (EC 3.6.4.6) (VESICULAR-FUSION PROTEIN NSF) (N- ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN) (NEM-SENSITIVE FUSION PROTEIN). [SWISSPROT;Acc:P46459] 0.66831 0.23765917
1709 0.933253 PSMC2 26S PROTEASE REGULATORY SUBUNIT 7 (MSS1 PROTEIN). [SWISSPROT;Acc:P35998] 3.92714 0.237641897
1710 0.83123 RPL4 60S RIBOSOMAL PROTEIN L4 (L1). [SWISSPROT;Acc:P36578] 3.49797 0.237632112
1711 0.18248 PNPLA7 0.768033 0.237593958
1712 0.667497 PSMD11 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 11 (26S PROTEASOME REGULATORY SUBUNIT S9) (26S PROTEASOME REGULATORY SUBUNIT P44.5). [SWISSPROT;Acc:O00231] 2.81169 0.237400638
1713 0.750885 PSMD6 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 6 (26S PROTEASOME REGULATORY SUBUNIT S10) (P42A) (PROTEASOME REGULATORY PARTICLE SUBUNIT P44S10). [SWISSPROT;Acc:Q15008] 3.16322 0.237379948
1714 0.0909039 NOLA2 "NUCLEOLAR PROTEIN FAMILY A, MEMBER 2; COMPONENT OF THE H/ACA SNORNP. [RefSeq;Acc:NM_017838]" 0.382985 0.237356293
1715 0.0303013 GTF2F1 "TRANSCRIPTION INITIATION FACTOR IIF, ALPHA SUBUNIT (TFIIF-ALPHA) (TRANSCRIPTION INITIATION FACTOR RAP74). [SWISSPROT;Acc:P35269]" 0.127662 0.237355674
1716 0.269961 ATP6V0A1 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] 1.13756 0.237315834
1717 0.224133 ATP6V0A4 "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" 0.944489 0.237306099
1718 0.211834 ATP6V0A2 VACUOLAR PROTON TRANSLOCATING ATPASE 116 KDA SUBUNIT A ISOFORM 2 (V-ATPASE 116-KDA ISOFORM A2) (TJ6). [SWISSPROT;Acc:Q9Y487] 0.892673 0.237303021
1719 0.202198 TCIRG1 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 0.852079 0.237299593
1720 0.321031 MDN1 MIDASIN (MIDAS-CONTAINING PROTEIN). [SWISSPROT;Acc:Q9NU22] 1.35288 0.237294512
1721 0.154828 PSMD9 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 9 (26S PROTEASOME REGULATORY SUBUNIT P27). [SWISSPROT;Acc:O00233] 0.652697 0.237212673
1722 0.367472 DIMT1L "PROBABLE DIMETHYLADENOSINE TRANSFERASE (EC 2.1.1.-) (S- ADENOSYLMETHIONINE-6-N',N'-ADENOSYL(RRNA) DIMETHYLTRANSFERASE) (18S RRNA DIMETHYLASE). [SWISSPROT;Acc:Q9UNQ2]" 1.54946 0.237161334
1723 0.230384 VPS45 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 45 (H-VPS45) (HLVPS45). [SWISSPROT;Acc:Q9NRW7] 0.971531 0.237134996
1724 0.0547796 RIOK2 0.231086 0.237052872
1725 0.10685 VPS25 0.450769 0.23703937
1726 CHMP6
1727 0.0175982 GAD2 "GLUTAMATE DECARBOXYLASE, 65 KDA ISOFORM (EC 4.1.1.15) (GAD-65) (65 KDA GLUTAMIC ACID DECARBOXYLASE). [SWISSPROT;Acc:Q05329]" 0.0742417 0.237039292
1728 0.0787698 C12orf26 0.332307 0.237039244
1729 0.056545 NAPG "GAMMA-SOLUBLE NSF ATTACHMENT PROTEIN (SNAP-GAMMA) (N-ETHYLMALEIMIDE- SENSITIVE FACTOR ATTACHMENT PROTEIN, GAMMA). [SWISSPROT;Acc:Q99747]" 0.238547 0.237039242
1730 0.02137 NOSTRIN NOSTRIN. [RefSeq;Acc:NM_052946] 0.0901539 0.237039108
1731 no value
1732 0.0213112 GAD1 "GLUTAMATE DECARBOXYLASE, 67 KDA ISOFORM (EC 4.1.1.15) (GAD-67) (67 KDA GLUTAMIC ACID DECARBOXYLASE). [SWISSPROT;Acc:Q99259]" 0.0899059 0.237038949
1733 0.0166846 SLC39A6 "LIV-1 PROTEIN, ESTROGEN REGULATED. [RefSeq;Acc:NM_012319]" 0.0703876 0.23703891
1734 0.04274 SNF8 EAP30 SUBUNIT OF ELL COMPLEX. [RefSeq;Acc:NM_007241] 0.180308 0.237038845
1735 0.180241 RAD54L RAD54-LIKE PROTEIN; RAD54 HOMOLOG. [RefSeq;Acc:NM_003579] 0.760447 0.237019805
1736 0.630807 ATPBD3 2.66198 0.236969098
1737 0.094576 QRSL1 GLUTAMINYL-TRNA SYNTHASE (GLUTAMINE-HYDROLYZING)-LIKE 1. [RefSeq;Acc:NM_018292] 0.399107 0.236969033
1738 0.0947181 FAAH FATTY-ACID AMIDE HYDROLASE (EC 3.1.-.-) (OLEAMIDE HYDROLASE) (ANANDAMIDE AMIDOHYDROLASE). [SWISSPROT;Acc:O00519] 0.399707 0.23696883
1739 0.0946707 UNG "URACIL-DNA GLYCOSYLASE, MITOCHONDRIAL PRECURSOR (EC 3.2.2.-) (UDG). [SWISSPROT;Acc:P13051]" 0.399507 0.236968814
1740 PET112L "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]"
1741 0.0315727 COTL1 COACTOSIN-LIKE PROTEIN. [SWISSPROT;Acc:Q14019] 0.133236 0.236968237
1742 0.0676104 COG6 CONSERVED OLIGOMERIC GOLGI COMPLEX COMPONENT 6. [SWISSPROT;Acc:Q9Y2V7] 0.2855 0.236814011
1743 0.229236 no value 40S RIBOSOMAL PROTEIN S28. [SWISSPROT;Acc:P25112] 0.968071 0.236796681
1744 0.357744 ATP6V1B2 "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]" 1.51127 0.236717463
1745 0.0826697 GDAP1L1 GANGLIOSIDE-INDUCED DIFFERENTIATION-ASSOCIATED PROTEIN 1-LIKE 1. [RefSeq;Acc:NM_024034] 0.349234 0.236717215
1746 0.134029 SEC31A YEAST SEC31P HOMOLOG. [RefSeq;Acc:NM_014933] 0.566199 0.236717126
1747 0.480242 ATP6V1E1 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] 2.02876 0.236717009
1748 0.0973611 GDAP1 GANGLIOSIDE-INDUCED DIFFERENTIATION-ASSOCIATED PROTEIN 1. [RefSeq;Acc:NM_018972] 0.411298 0.236716687
1749 0.518099 ATP6V1D 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] 2.18869 0.236716483
1750 0.0562476 ATP6V1H 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] 0.237616 0.236716383
1751 0.0861167 no value VACUOLAR ATP SYNTHASE SUBUNIT G 2 (EC 3.6.3.14) (V-ATPASE G SUBUNIT 2) (VACUOLAR PROTON PUMP G SUBUNIT 2) (V-ATPASE 13 KDA SUBUNIT 2). [SWISSPROT;Acc:O95670] 0.363797 0.236716356
1752 0.107954 SEC31B SECRETORY PATHWAY COMPONENT SEC31B-1. [RefSeq;Acc:NM_015490] 0.456048 0.236716311
1753 0.126518 SEC13 SEC13-RELATED PROTEIN. [SWISSPROT;Acc:P55735] 0.534471 0.236716305
1754 0.0486762 ATP6V1G3 VACUOLAR ATP SYNTHASE SUBUNIT G 3 (EC 3.6.3.14) (V-ATPASE G SUBUNIT 3) (VACUOLAR PROTON PUMP G SUBUNIT 3) (V-ATPASE 13 KDA SUBUNIT 3). [SWISSPROT;Acc:Q96LB4] 0.205631 0.236716254
1755 0.0646874 API5 APOPTOSIS INHIBITOR 5; FIBROBLAST GROWTH FACTOR 2-INTERACTING FACTOR 2; API5-LIKE 1. [RefSeq;Acc:NM_006595] 0.27327 0.236716068
1756 0.063055 ATP6V1G1 VACUOLAR ATP SYNTHASE SUBUNIT G 1 (EC 3.6.3.14) (V-ATPASE G SUBUNIT 1) (VACUOLAR PROTON PUMP G SUBUNIT 1) (V-ATPASE 13 KDA SUBUNIT 1) (VACUOLAR ATP SYNTHASE SUBUNIT M16). [SWISSPROT;Acc:O75348] 0.266374 0.236716046
1757 0.420128 ATP6V1E2 1.77482 0.236715836

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/