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 description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 1658 to 1707 of 3206 in total
Rank
description
measured
expected
final
Hugo
1658 TRIPARTITE MOTIF PROTEIN 3 (RING FINGER PROTEIN 22) (BRAIN-EXPRESSED RING FINGER PROTEIN). [SWISSPROT;Acc:O75382] 0.271838 1.13816 0.238839882 TRIM3
1659 TCD37 HOMOLOG; PRUNE. [RefSeq;Acc:NM_021222] 0.118202 0.494902 0.238839205 PRUNE
1660 CYCLIN M4; ANCIENT CONSERVED DOMAIN PROTEIN 4. [RefSeq;Acc:NM_020184] 0.285611 1.19583 0.238839133 CNNM4
1661 COPPER-TRANSPORTING ATPASE 2 (EC 3.6.3.4) (COPPER PUMP 2) (WILSON DISEASE-ASSOCIATED PROTEIN). [SWISSPROT;Acc:P35670] 0.0958705 0.401402 0.238839119 ATP7B
1662 0.0879782 0.368359 0.238838199 PRUNE2
1663 CYCLIN M1; ANCIENT CONSERVED DOMAIN PROTEIN 1. [RefSeq;Acc:NM_020348] 0.264548 1.10767 0.238832865 CNNM1
1664 CYCLIN M3; ANCIENT CONSERVED DOMAIN PROTEIN 3. [RefSeq;Acc:NM_017623] 0.258494 1.08234 0.238828834 CNNM3
1665 "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 0.752395 0.238801427 PPP1R8
1666 44050 PROTEIN. [RefSeq;Acc:NM_178832] 0.03729 0.156155 0.238801191 C10orf83
1667 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 4.005 0.238773783 PSMA3
1668 MESODERM INDUCTION EARLY RESPONSE 1. [RefSeq;Acc:NM_020948] 0.0415385 0.173966 0.238773668 no value
1669 DEPDC5
1670 0.0336981 0.14113 0.238773471 MIER3
1671 0.0335839 0.140652 0.238773 MIER2
1672 "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 1.10501 0.238410512 SFPQ
1673 0.847098 3.55339 0.238391508 IMP3
1674 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 10 (26S PROTEASOME REGULATORY SUBUNIT P28) (GANKYRIN). [SWISSPROT;Acc:O75832] 0.41158 1.7269 0.238334588 PSMD10
1675 PARASPECKLE PROTEIN 1. [RefSeq;Acc:NM_018282] 0.203402 0.853581 0.238292558 PSPC1
1676 "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 0.847008 0.238289367 NONO
1677 0.461707 1.93809 0.238227843 KCTD17
1678 0.581959 2.44287 0.238227577 KCTD5
1679 0.48192 2.02294 0.23822753 KCTD2
1680 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 12 (26S PROTEASOME REGULATORY SUBUNIT P55). [SWISSPROT;Acc:O00232] 0.563839 2.36701 0.238207274 no value
1681 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 0.0944225 0.238166751 ALDH18A1
1682 NICOTINAMIDE NUCLEOTIDE ADENYLYLTRANSFERASE 3; PYRIDINE NUCLEOTIDE ADENYLYLTRANSFERASE 3. [RefSeq;Acc:NM_178177] 0.192536 0.808409 0.238166572 NMNAT3
1683 NUCLEOLAR PROTEIN NOP5 (NUCLEOLAR PROTEIN 5) (NOP58) (HSPC120). [SWISSPROT;Acc:Q9Y2X3] 0.160247 0.672842 0.238164383 no value
1684 60S RIBOSOMAL PROTEIN L37 (G1.16). [SWISSPROT;Acc:P02403] 0.0238444 0.100146 0.238096379 RPL37
1685 "SPLICING FACTOR, ARGININE/SERINE-RICH 1 (PRE-MRNA SPLICING FACTOR SF2, P33 SUBUNIT) (ALTERNATIVE SPLICING FACTOR ASF-1). [SWISSPROT;Acc:Q07955]" SFRS1
1686 SORTING NEXIN 17. [SWISSPROT;Acc:Q15036] 0.0476887 0.200292 0.23809588 SNX17
1687 AMIDOPHOSPHORIBOSYLTRANSFERASE PRECURSOR (EC 2.4.2.14) (GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE) (ATASE) (GPAT). [SWISSPROT;Acc:Q06203] 0.214575 0.901215 0.238095238 PPAT
1688 SERINE/THREONINE-PROTEIN KINASE NEK3 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 3) (HSPK 36). [SWISSPROT;Acc:P51956] 0.0267969 0.112547 0.238095196 NEK3
1689 "GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE, LIVER (EC 1.2.1.12) (GAPDH). [SWISSPROT;Acc:P04406]" 0.414602 1.74133 0.238095019 GAPDH
1690 SERINE/THREONINE-PROTEIN KINASE NEK1 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 1) (NY-REN-55 ANTIGEN). [SWISSPROT;Acc:Q96PY6] 0.035086 0.147362 0.238093946 NEK1
1691 PUTATIVE INORGANIC POLYPHOSPHATE/ATP-NAD KINASE (EC 2.7.1.23) (POLY(P)/ATP NAD KINASE). [SWISSPROT;Acc:O95544] 0.195442 0.821038 0.238042575 NADK
1692 "ADP,ATP CARRIER PROTEIN, FIBROBLAST ISOFORM (ADP/ATP TRANSLOCASE 2) (ADENINE NUCLEOTIDE TRANSLOCATOR 2) (ANT 2). [SWISSPROT;Acc:P05141]" 0.032514 0.136688 0.237870186 SLC25A5
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 DYNACTIN COMPLEX 50 KDA SUBUNIT (50 KDA DYNEIN-ASSOCIATED POLYPEPTIDE) (DYNAMITIN) (DCTN-50) (DYNACTIN 2). [SWISSPROT;Acc:Q13561] 0.375423 1.57827 0.237869946 DCTN2
1695 0.0256535 0.107847 0.237869389 SLC25A31
1696 "ADP,ATP CARRIER PROTEIN, LIVER ISOFORM T2 (ADP/ATP TRANSLOCASE 3) (ADENINE NUCLEOTIDE TRANSLOCATOR 3) (ANT 3). [SWISSPROT;Acc:P12236]" 0.0311972 0.131153 0.237868749 SLC25A6
1697 ASPARAGINE SYNTHETASE [GLUTAMINE-HYDROLYZING] (EC 6.3.5.4) (GLUTAMINE- DEPENDENT ASPARAGINE SYNTHETASE) (TS11 CELL CYCLE CONTROL PROTEIN). [SWISSPROT;Acc:P08243] 0.0326245 0.137154 0.237867652 ASNS
1698 "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 2.99562 0.23786762 ATP6V1A
1699 HCV NS3-TRANSACTIVATED PROTEIN 1. [RefSeq;Acc:NM_019048] 0.0338955 0.142498 0.237866496 ASNSD1
1700 0.044904 0.188793 0.237847802 no value
1701 NEMO-LIKE KINASE; LIKELY ORTHOLOG OF MOUSE NEMO LIKE KINASE. [RefSeq;Acc:NM_016231] 0.210207 0.883788 0.237847764 NLK
1702 ELKS PROTEIN. [RefSeq;Acc:NM_015064] 0.0412444 0.173407 0.237847376 ERC1
1703 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 3 (26S PROTEASOME REGULATORY SUBUNIT S3) (PROTEASOME SUBUNIT P58). [SWISSPROT;Acc:O43242] 0.779642 3.27908 0.237762421 PSMD3
1704 DJ408B20.3 (NOVEL PROTEIN SIMILAR TO 60S ACIDIC RIBOSOMAL PROTEIN P2 (RPLP2)). [SPTREMBL;Acc:Q9H5A9] 0.0573148 0.241075 0.237746759 no value
1705 BETA-CENTRACTIN (ACTIN-RELATED PROTEIN 1B) (ARP1B). [SWISSPROT;Acc:P42025] 0.0916612 0.385556 0.237737709 ACTR1B
1706 ALPHA-CENTRACTIN (CENTRACTIN) (CENTROSOME-ASSOCIATED ACTIN HOMOLOG) (ACTIN-RPV) (ARP1). [SWISSPROT;Acc:P42024] 0.0967911 0.407134 0.237737698 ACTR1A
1707 26S PROTEASE REGULATORY SUBUNIT 6B (MIP224) (MB67 INTERACTING PROTEIN) (TAT-BINDING PROTEIN-7) (TBP-7). [SWISSPROT;Acc:P43686] 0.848985 3.57194 0.237681764 PSMC4

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/