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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final Gene expected Rank measured description Hugo
Results: HTML CSV LaTeX Showing element 1502 to 1551 of 3206 in total
final
expected
Rank
measured
description
Hugo
0.237737709 0.385556 1705 0.0916612 BETA-CENTRACTIN (ACTIN-RELATED PROTEIN 1B) (ARP1B). [SWISSPROT;Acc:P42025] ACTR1B
0.237746759 0.241075 1704 0.0573148 DJ408B20.3 (NOVEL PROTEIN SIMILAR TO 60S ACIDIC RIBOSOMAL PROTEIN P2 (RPLP2)). [SPTREMBL;Acc:Q9H5A9] no value
0.237762421 3.27908 1703 0.779642 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 3 (26S PROTEASOME REGULATORY SUBUNIT S3) (PROTEASOME SUBUNIT P58). [SWISSPROT;Acc:O43242] PSMD3
0.237847376 0.173407 1702 0.0412444 ELKS PROTEIN. [RefSeq;Acc:NM_015064] ERC1
0.237847764 0.883788 1701 0.210207 NEMO-LIKE KINASE; LIKELY ORTHOLOG OF MOUSE NEMO LIKE KINASE. [RefSeq;Acc:NM_016231] NLK
0.237847802 0.188793 1700 0.044904 no value
0.237866496 0.142498 1699 0.0338955 HCV NS3-TRANSACTIVATED PROTEIN 1. [RefSeq;Acc:NM_019048] ASNSD1
0.23786762 2.99562 1698 0.712561 "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]" ATP6V1A
0.237867652 0.137154 1697 0.0326245 ASPARAGINE SYNTHETASE [GLUTAMINE-HYDROLYZING] (EC 6.3.5.4) (GLUTAMINE- DEPENDENT ASPARAGINE SYNTHETASE) (TS11 CELL CYCLE CONTROL PROTEIN). [SWISSPROT;Acc:P08243] ASNS
0.237868749 0.131153 1696 0.0311972 "ADP,ATP CARRIER PROTEIN, LIVER ISOFORM T2 (ADP/ATP TRANSLOCASE 3) (ADENINE NUCLEOTIDE TRANSLOCATOR 3) (ANT 3). [SWISSPROT;Acc:P12236]" SLC25A6
0.237869389 0.107847 1695 0.0256535 SLC25A31
0.237869946 1.57827 1694 0.375423 DYNACTIN COMPLEX 50 KDA SUBUNIT (50 KDA DYNEIN-ASSOCIATED POLYPEPTIDE) (DYNAMITIN) (DCTN-50) (DYNACTIN 2). [SWISSPROT;Acc:Q13561] DCTN2
0.237870186 0.136688 1692 0.032514 "ADP,ATP CARRIER PROTEIN, FIBROBLAST ISOFORM (ADP/ATP TRANSLOCASE 2) (ADENINE NUCLEOTIDE TRANSLOCATOR 2) (ANT 2). [SWISSPROT;Acc:P05141]" 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
0.238042575 0.821038 1691 0.195442 PUTATIVE INORGANIC POLYPHOSPHATE/ATP-NAD KINASE (EC 2.7.1.23) (POLY(P)/ATP NAD KINASE). [SWISSPROT;Acc:O95544] NADK
0.238093946 0.147362 1690 0.035086 SERINE/THREONINE-PROTEIN KINASE NEK1 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 1) (NY-REN-55 ANTIGEN). [SWISSPROT;Acc:Q96PY6] NEK1
0.238095019 1.74133 1689 0.414602 "GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE, LIVER (EC 1.2.1.12) (GAPDH). [SWISSPROT;Acc:P04406]" GAPDH
0.238095196 0.112547 1688 0.0267969 SERINE/THREONINE-PROTEIN KINASE NEK3 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 3) (HSPK 36). [SWISSPROT;Acc:P51956] NEK3
0.238095238 0.901215 1687 0.214575 AMIDOPHOSPHORIBOSYLTRANSFERASE PRECURSOR (EC 2.4.2.14) (GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE) (ATASE) (GPAT). [SWISSPROT;Acc:Q06203] PPAT
0.23809588 0.200292 1686 0.0476887 SORTING NEXIN 17. [SWISSPROT;Acc:Q15036] SNX17
0.238096379 0.100146 1684 0.0238444 60S RIBOSOMAL PROTEIN L37 (G1.16). [SWISSPROT;Acc:P02403] RPL37
1685 "SPLICING FACTOR, ARGININE/SERINE-RICH 1 (PRE-MRNA SPLICING FACTOR SF2, P33 SUBUNIT) (ALTERNATIVE SPLICING FACTOR ASF-1). [SWISSPROT;Acc:Q07955]" SFRS1
0.238164383 0.672842 1683 0.160247 NUCLEOLAR PROTEIN NOP5 (NUCLEOLAR PROTEIN 5) (NOP58) (HSPC120). [SWISSPROT;Acc:Q9Y2X3] no value
0.238166572 0.808409 1682 0.192536 NICOTINAMIDE NUCLEOTIDE ADENYLYLTRANSFERASE 3; PYRIDINE NUCLEOTIDE ADENYLYLTRANSFERASE 3. [RefSeq;Acc:NM_178177] NMNAT3
0.238166751 0.0944225 1681 0.0224883 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 ALDH18A1
0.238207274 2.36701 1680 0.563839 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 12 (26S PROTEASOME REGULATORY SUBUNIT P55). [SWISSPROT;Acc:O00232] no value
0.23822753 2.02294 1679 0.48192 KCTD2
0.238227577 2.44287 1678 0.581959 KCTD5
0.238227843 1.93809 1677 0.461707 KCTD17
0.238289367 0.847008 1676 0.201833 "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]" NONO
0.238292558 0.853581 1675 0.203402 PARASPECKLE PROTEIN 1. [RefSeq;Acc:NM_018282] PSPC1
0.238334588 1.7269 1674 0.41158 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 10 (26S PROTEASOME REGULATORY SUBUNIT P28) (GANKYRIN). [SWISSPROT;Acc:O75832] PSMD10
0.238391508 3.55339 1673 0.847098 IMP3
0.238410512 1.10501 1672 0.263446 "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]" SFPQ
0.238773 0.140652 1671 0.0335839 MIER2
0.238773471 0.14113 1670 0.0336981 MIER3
0.238773668 0.173966 1668 0.0415385 MESODERM INDUCTION EARLY RESPONSE 1. [RefSeq;Acc:NM_020948] no value
1669 DEPDC5
0.238773783 4.005 1667 0.956289 PROTEASOME SUBUNIT ALPHA TYPE 3 (EC 3.4.25.1) (PROTEASOME COMPONENT C8) (MACROPAIN SUBUNIT C8) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C8). [SWISSPROT;Acc:P25788] PSMA3
0.238801191 0.156155 1666 0.03729 44050 PROTEIN. [RefSeq;Acc:NM_178832] C10orf83
0.238801427 0.752395 1665 0.179673 "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]" PPP1R8
0.238828834 1.08234 1664 0.258494 CYCLIN M3; ANCIENT CONSERVED DOMAIN PROTEIN 3. [RefSeq;Acc:NM_017623] CNNM3
0.238832865 1.10767 1663 0.264548 CYCLIN M1; ANCIENT CONSERVED DOMAIN PROTEIN 1. [RefSeq;Acc:NM_020348] CNNM1
0.238838199 0.368359 1662 0.0879782 PRUNE2
0.238839119 0.401402 1661 0.0958705 COPPER-TRANSPORTING ATPASE 2 (EC 3.6.3.4) (COPPER PUMP 2) (WILSON DISEASE-ASSOCIATED PROTEIN). [SWISSPROT;Acc:P35670] ATP7B
0.238839133 1.19583 1660 0.285611 CYCLIN M4; ANCIENT CONSERVED DOMAIN PROTEIN 4. [RefSeq;Acc:NM_020184] CNNM4
0.238839205 0.494902 1659 0.118202 TCD37 HOMOLOG; PRUNE. [RefSeq;Acc:NM_021222] PRUNE
0.238839882 1.13816 1658 0.271838 TRIPARTITE MOTIF PROTEIN 3 (RING FINGER PROTEIN 22) (BRAIN-EXPRESSED RING FINGER PROTEIN). [SWISSPROT;Acc:O75382] TRIM3
0.238849597 1.3291 1657 0.317455 CYCLIN M2; ANCIENT CONSERVED DOMAIN PROTEIN 2. [RefSeq;Acc:NM_017649] CNNM2
0.238850131 0.337708 1656 0.0806616 COPPER-TRANSPORTING ATPASE 1 (EC 3.6.3.4) (COPPER PUMP 1) (MENKES DISEASE-ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q04656] ATP7A

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/