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 1651 to 1700 of 3206 in total
Rank
expected
description
measured
Hugo
final
1651 0.142333 AARF DOMAIN CONTAINING KINASE 1. [RefSeq;Acc:NM_020421] 0.0340138 ADCK1 0.238973393
1652 AARF DOMAIN CONTAINING KINASE 2; PUTATIVE UBIQUINONE BIOSYNTHESIS PROTEIN AARF. [RefSeq;Acc:NM_052853] ADCK2
1653 0.115005 AARF DOMAIN CONTAINING KINASE 4. [RefSeq;Acc:NM_024876] 0.0274831 ADCK4 0.238973088
1654 3.16764 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 13 (26S PROTEASOME REGULATORY SUBUNIT S11) (26S PROTEASOME REGULATORY SUBUNIT P40.5). [SWISSPROT;Acc:Q9UNM6] 0.75685 PSMD13 0.238931823
1655 0.305877 APURINIC/APYRIMIDINIC ENDONUCLEASE 2; APURINIC/APYRIMIDINIC ENDONUCLEASE-LIKE 2; APEX NUCLEASE-LIKE 2. [RefSeq;Acc:NM_014481] 0.0730689 APEX2 0.238883277
1656 0.337708 COPPER-TRANSPORTING ATPASE 1 (EC 3.6.3.4) (COPPER PUMP 1) (MENKES DISEASE-ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q04656] 0.0806616 ATP7A 0.238850131
1657 1.3291 CYCLIN M2; ANCIENT CONSERVED DOMAIN PROTEIN 2. [RefSeq;Acc:NM_017649] 0.317455 CNNM2 0.238849597
1658 1.13816 TRIPARTITE MOTIF PROTEIN 3 (RING FINGER PROTEIN 22) (BRAIN-EXPRESSED RING FINGER PROTEIN). [SWISSPROT;Acc:O75382] 0.271838 TRIM3 0.238839882
1659 0.494902 TCD37 HOMOLOG; PRUNE. [RefSeq;Acc:NM_021222] 0.118202 PRUNE 0.238839205
1660 1.19583 CYCLIN M4; ANCIENT CONSERVED DOMAIN PROTEIN 4. [RefSeq;Acc:NM_020184] 0.285611 CNNM4 0.238839133
1661 0.401402 COPPER-TRANSPORTING ATPASE 2 (EC 3.6.3.4) (COPPER PUMP 2) (WILSON DISEASE-ASSOCIATED PROTEIN). [SWISSPROT;Acc:P35670] 0.0958705 ATP7B 0.238839119
1662 0.368359 0.0879782 PRUNE2 0.238838199
1663 1.10767 CYCLIN M1; ANCIENT CONSERVED DOMAIN PROTEIN 1. [RefSeq;Acc:NM_020348] 0.264548 CNNM1 0.238832865
1664 1.08234 CYCLIN M3; ANCIENT CONSERVED DOMAIN PROTEIN 3. [RefSeq;Acc:NM_017623] 0.258494 CNNM3 0.238828834
1665 0.752395 "NUCLEAR INHIBITOR OF PROTEIN PHOSPHATASE-1 (NIPP-1) (PROTEIN PHOSPHATASE 1, REGULATORY INHIBITOR SUBUNIT 8) [INCLUDES: ACTIVATOR OF RNA DECAY (EC 3.1.4.-) (ARD-1)]. [SWISSPROT;Acc:Q12972]" 0.179673 PPP1R8 0.238801427
1666 0.156155 44050 PROTEIN. [RefSeq;Acc:NM_178832] 0.03729 C10orf83 0.238801191
1667 4.005 PROTEASOME SUBUNIT ALPHA TYPE 3 (EC 3.4.25.1) (PROTEASOME COMPONENT C8) (MACROPAIN SUBUNIT C8) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C8). [SWISSPROT;Acc:P25788] 0.956289 PSMA3 0.238773783
1668 0.173966 MESODERM INDUCTION EARLY RESPONSE 1. [RefSeq;Acc:NM_020948] 0.0415385 no value 0.238773668
1669 DEPDC5
1670 0.14113 0.0336981 MIER3 0.238773471
1671 0.140652 0.0335839 MIER2 0.238773
1672 1.10501 "SPLICING FACTOR, PROLINE-AND GLUTAMINE-RICH (POLYPYRIMIDINE TRACT- BINDING PROTEIN-ASSOCIATED SPLICING FACTOR) (PTB-ASSOCIATED SPLICING FACTOR) (PSF) (DNA-BINDING P52/P100 COMPLEX, 100 KDA SUBUNIT). [SWISSPROT;Acc:P23246]" 0.263446 SFPQ 0.238410512
1673 3.55339 0.847098 IMP3 0.238391508
1674 1.7269 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 10 (26S PROTEASOME REGULATORY SUBUNIT P28) (GANKYRIN). [SWISSPROT;Acc:O75832] 0.41158 PSMD10 0.238334588
1675 0.853581 PARASPECKLE PROTEIN 1. [RefSeq;Acc:NM_018282] 0.203402 PSPC1 0.238292558
1676 0.847008 "54 KDA NUCLEAR RNA- AND DNA-BINDING PROTEIN (P54(NRB)) (P54NRB) (55 KDA NUCLEAR PROTEIN) (NMT55) (NON-POU DOMAIN-CONTAINING OCTAMER- BINDING PROTEIN) (DNA-BINDING P52/P100 COMPLEX, 52 KDA SUBUNIT). [SWISSPROT;Acc:Q15233]" 0.201833 NONO 0.238289367
1677 1.93809 0.461707 KCTD17 0.238227843
1678 2.44287 0.581959 KCTD5 0.238227577
1679 2.02294 0.48192 KCTD2 0.23822753
1680 2.36701 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 12 (26S PROTEASOME REGULATORY SUBUNIT P55). [SWISSPROT;Acc:O00232] 0.563839 no value 0.238207274
1681 0.0944225 DELTA 1-PYRROLINE-5-CARBOXYLATE SYNTHETASE (P5CS) [INCLUDES: GLUTAMATE 5-KINASE (EC 2.7.2.11) (GAMMA-GLUTAMYL KINASE) (GK); GAMMA-GLUTAMYL PHOSPHATE REDUCTASE (GPR) (EC 1.2.1.41) (GLUTAMATE-5-SEMIALDEHYDE DEHYDROGENASE) (GLUTAMYL-GAMMA-SEMIALDEHYDE DEHYDR 0.0224883 ALDH18A1 0.238166751
1682 0.808409 NICOTINAMIDE NUCLEOTIDE ADENYLYLTRANSFERASE 3; PYRIDINE NUCLEOTIDE ADENYLYLTRANSFERASE 3. [RefSeq;Acc:NM_178177] 0.192536 NMNAT3 0.238166572
1683 0.672842 NUCLEOLAR PROTEIN NOP5 (NUCLEOLAR PROTEIN 5) (NOP58) (HSPC120). [SWISSPROT;Acc:Q9Y2X3] 0.160247 no value 0.238164383
1684 0.100146 60S RIBOSOMAL PROTEIN L37 (G1.16). [SWISSPROT;Acc:P02403] 0.0238444 RPL37 0.238096379
1685 "SPLICING FACTOR, ARGININE/SERINE-RICH 1 (PRE-MRNA SPLICING FACTOR SF2, P33 SUBUNIT) (ALTERNATIVE SPLICING FACTOR ASF-1). [SWISSPROT;Acc:Q07955]" SFRS1
1686 0.200292 SORTING NEXIN 17. [SWISSPROT;Acc:Q15036] 0.0476887 SNX17 0.23809588
1687 0.901215 AMIDOPHOSPHORIBOSYLTRANSFERASE PRECURSOR (EC 2.4.2.14) (GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE) (ATASE) (GPAT). [SWISSPROT;Acc:Q06203] 0.214575 PPAT 0.238095238
1688 0.112547 SERINE/THREONINE-PROTEIN KINASE NEK3 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 3) (HSPK 36). [SWISSPROT;Acc:P51956] 0.0267969 NEK3 0.238095196
1689 1.74133 "GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE, LIVER (EC 1.2.1.12) (GAPDH). [SWISSPROT;Acc:P04406]" 0.414602 GAPDH 0.238095019
1690 0.147362 SERINE/THREONINE-PROTEIN KINASE NEK1 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 1) (NY-REN-55 ANTIGEN). [SWISSPROT;Acc:Q96PY6] 0.035086 NEK1 0.238093946
1691 0.821038 PUTATIVE INORGANIC POLYPHOSPHATE/ATP-NAD KINASE (EC 2.7.1.23) (POLY(P)/ATP NAD KINASE). [SWISSPROT;Acc:O95544] 0.195442 NADK 0.238042575
1692 0.136688 "ADP,ATP CARRIER PROTEIN, FIBROBLAST ISOFORM (ADP/ATP TRANSLOCASE 2) (ADENINE NUCLEOTIDE TRANSLOCATOR 2) (ANT 2). [SWISSPROT;Acc:P05141]" 0.032514 SLC25A5 0.237870186
1693 "ADP,ATP CARRIER PROTEIN, HEART/SKELETAL MUSCLE ISOFORM T1 (ADP/ATP TRANSLOCASE 1) (ADENINE NUCLEOTIDE TRANSLOCATOR 1) (ANT 1). [SWISSPROT;Acc:P12235]" SLC25A4
1694 1.57827 DYNACTIN COMPLEX 50 KDA SUBUNIT (50 KDA DYNEIN-ASSOCIATED POLYPEPTIDE) (DYNAMITIN) (DCTN-50) (DYNACTIN 2). [SWISSPROT;Acc:Q13561] 0.375423 DCTN2 0.237869946
1695 0.107847 0.0256535 SLC25A31 0.237869389
1696 0.131153 "ADP,ATP CARRIER PROTEIN, LIVER ISOFORM T2 (ADP/ATP TRANSLOCASE 3) (ADENINE NUCLEOTIDE TRANSLOCATOR 3) (ANT 3). [SWISSPROT;Acc:P12236]" 0.0311972 SLC25A6 0.237868749
1697 0.137154 ASPARAGINE SYNTHETASE [GLUTAMINE-HYDROLYZING] (EC 6.3.5.4) (GLUTAMINE- DEPENDENT ASPARAGINE SYNTHETASE) (TS11 CELL CYCLE CONTROL PROTEIN). [SWISSPROT;Acc:P08243] 0.0326245 ASNS 0.237867652
1698 2.99562 "VACUOLAR ATP SYNTHASE CATALYTIC SUBUNIT A, UBIQUITOUS ISOFORM (EC 3.6.3.14) (V-ATPASE A SUBUNIT 1) (VACUOLAR PROTON PUMP ALPHA SUBUNIT 1) (V-ATPASE 69 KDA SUBUNIT 1) (ISOFORM VA68). [SWISSPROT;Acc:P38606]" 0.712561 ATP6V1A 0.23786762
1699 0.142498 HCV NS3-TRANSACTIVATED PROTEIN 1. [RefSeq;Acc:NM_019048] 0.0338955 ASNSD1 0.237866496
1700 0.188793 0.044904 no value 0.237847802

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/