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 1552 to 1601 of 3206 in total
final
expected
Rank
measured
description
Hugo
0.238883277 0.305877 1655 0.0730689 APURINIC/APYRIMIDINIC ENDONUCLEASE 2; APURINIC/APYRIMIDINIC ENDONUCLEASE-LIKE 2; APEX NUCLEASE-LIKE 2. [RefSeq;Acc:NM_014481] APEX2
0.238931823 3.16764 1654 0.75685 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 13 (26S PROTEASOME REGULATORY SUBUNIT S11) (26S PROTEASOME REGULATORY SUBUNIT P40.5). [SWISSPROT;Acc:Q9UNM6] PSMD13
0.238973088 0.115005 1653 0.0274831 AARF DOMAIN CONTAINING KINASE 4. [RefSeq;Acc:NM_024876] ADCK4
0.238973393 0.142333 1650 0.0340138 "CHAPERONE-ACTIVITY OF BC1 COMPLEX-LIKE, MITOCHONDRIAL PRECURSOR (CHAPERONE-ABC1-LIKE). [SWISSPROT;Acc:Q8NI60]" CABC1
1651 AARF DOMAIN CONTAINING KINASE 1. [RefSeq;Acc:NM_020421] ADCK1
1652 AARF DOMAIN CONTAINING KINASE 2; PUTATIVE UBIQUINONE BIOSYNTHESIS PROTEIN AARF. [RefSeq;Acc:NM_052853] ADCK2
0.238973501 1.47667 1649 0.352885 COQ5
0.239024002 0.23248 1648 0.0555683 INOSITOL POLYPHOSPHATE 5-PHOSPHATASE OCRL-1 (EC 3.1.3.36) (LOWE'S OCULOCEREBRORENAL SYNDROME PROTEIN). [SWISSPROT;Acc:Q01968] OCRL
0.23902401 0.11537 1647 0.0275762 no value
0.23902439 0.210535 1646 0.050323 MYOSIN VI. [SWISSPROT;Acc:Q9UM54]
0.239024447 0.514211 1645 0.122909 UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG B (HHR23B) (XP-C REPAIR COMPLEMENTING COMPLEX 58 KDA PROTEIN) (P58). [SWISSPROT;Acc:P54727] RAD23B
0.239024455 5.30247 1644 1.26742 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 (26S PROTEASOME REGULATORY SUBUNIT S5A) (RPN10) (MULTIUBIQUITIN CHAIN BINDING PROTEIN) (ANTISECRETORY FACTOR-1) (AF) (ASF). [SWISSPROT;Acc:P55036] PSMD4
0.239024512 0.2611 1643 0.0624093 DDI1
0.239024545 0.204356 1642 0.0488461 no value
0.23902469 0.422881 1641 0.101079 UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A (HHR23A). [SWISSPROT;Acc:P54725] RAD23A
0.239052853 0.301896 1640 0.0721691 ALPHA-FETOPROTEIN ENHANCER BINDING PROTEIN (AT MOTIF-BINDING FACTOR) (AT-BINDING TRANSCRIPTION FACTOR 1). [SWISSPROT;Acc:Q15911] ZFHX3
0.239102009 3.30538 1639 0.790323 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 7 (26S PROTEASOME REGULATORY SUBUNIT S12) (PROTEASOME SUBUNIT P40) (MOV34 PROTEIN HOMOLOG). [SWISSPROT;Acc:P51665] PSMD7
0.239166175 3.20427 1638 0.766353 26S PROTEASE REGULATORY SUBUNIT 6A (TAT-BINDING PROTEIN 1) (TBP-1) (PROTEASOME SUBUNIT P50). [SWISSPROT;Acc:P17980] PSMC3
0.239178691 0.32156 1637 0.0769103 ZINC FINGER PROTEIN 207. [SWISSPROT;Acc:O43670] ZNF207
0.239179313 0.64312 1636 0.153821 MITOTIC CHECKPOINT PROTEIN BUB3. [SWISSPROT;Acc:O43684] BUB3
0.239189733 0.461922 1635 0.110487 INOSITOL-1(OR 4)-MONOPHOSPHATASE (EC 3.1.3.25) (IMPASE) (IMP) (INOSITOL MONOPHOSPHATASE) (LITHIUM-SENSITIVE MYO-INOSITOL MONOPHOSPHATASE A1). [SWISSPROT;Acc:P29218] IMPA1
0.239198381 0.384447 1634 0.0919591 INOSITOL-1(OR 4)-MONOPHOSPHATASE 2 (EC 3.1.3.25) (IMPASE 2) (IMP 2) (INOSITOL MONOPHOSPHATASE 2) (MYO-INOSITOL MONOPHOSPHATASE A2). [SWISSPROT;Acc:O14732] IMPA2
0.239199393 3.92552 1633 0.938982 KIAA0368
0.239287363 1.19135 1632 0.285075 TRIPARTITE MOTIF PROTEIN 2. [SWISSPROT;Acc:Q9C040] TRIM2
0.2392982 0.699345 1631 0.167352 PHLPP
0.239309392 0.551746 1630 0.132038 PHLPPL
0.239355394 1.63914 1629 0.392337 CAMP-DEPENDENT PROTEIN KINASE TYPE II-ALPHA REGULATORY CHAIN. [SWISSPROT;Acc:P13861] PRKAR2A
0.239365467 0.880269 1627 0.210706 "CAMP-DEPENDENT PROTEIN KINASE, BETA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-BETA). [SWISSPROT;Acc:P22694]" PRKACB
1628 "CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-ALPHA). [SWISSPROT;Acc:P17612]" PRKACA
0.239365758 0.796037 1626 0.190544 "CAMP-DEPENDENT PROTEIN KINASE, GAMMA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-GAMMA). [SWISSPROT;Acc:P22612]" PRKACG
0.239366197 0.598798 1625 0.143332 PROTEIN KINASE PKX1 (EC 2.7.1.-). [SWISSPROT;Acc:P51817] PRKX
0.239377235 1.40952 1624 0.337407 CAMP-DEPENDENT PROTEIN KINASE TYPE II-BETA REGULATORY CHAIN. [SWISSPROT;Acc:P31323] PRKAR2B
0.23959628 0.0681463 1623 0.0163276 ARHGAP10
0.239596518 0.0850893 1622 0.0203871 OLIGOPHRENIN-1 LIKE PROTEIN (GTPASE REGULATOR ASSOCIATED WITH FOCAL ADHESION KINASE). [SWISSPROT;Acc:Q9UNA1] ARHGAP26
0.239596694 0.62682 1621 0.150184 "CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL PRECURSOR (CYTOCHROME C-1). [SWISSPROT;Acc:P08574]" CYC1
0.239596836 0.302259 1620 0.0724203 SENESCENCE MARKER PROTEIN-30 (SMP-30) (REGUCALCIN) (RC). [SWISSPROT;Acc:Q15493] RGN
0.239597084 0.063934 1619 0.0153184 OLIGOPHRENIN 1. [SWISSPROT;Acc:O60890] OPHN1
0.239617307 0.35015 1618 0.083902 ACID CERAMIDASE PRECURSOR (EC 3.5.1.23) (ACYLSPHINGOSINE DEACYLASE) (N-ACYLSPHINGOSINE AMIDOHYDROLASE) (AC) (PUTATIVE 32 KDA HEART PROTEIN) (PHP32). [SWISSPROT;Acc:Q13510] ASAH1
0.239635283 0.160453 1616 0.0384502 MAEA
1617 RMND5A
0.239635594 0.641812 1615 0.153801 C20orf11
0.239730317 4.96583 1614 1.19046 26S PROTEASE REGULATORY SUBUNIT S10B (PROTEASOME SUBUNIT P42) (P44) (CONSERVED ATPASE DOMAIN PROTEIN 44) (CADP44). [SWISSPROT;Acc:Q92524] PSMC6
0.239731035 0.161954 1613 0.0388254 MITOCHONDRIAL RIBOSOMAL PROTEIN L30 ISOFORM A. [RefSeq;Acc:NM_145212] MRPL30
0.239803745 1.14341 1612 0.274194 "UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2; 1 ALPHA,25-DIHYDROXYVITAMIN D3-INDUCIBLE; ENTEROCYTE DIFFERENTIATION PROMOTING FACTOR; METHYL METHANESULFONATE SENSITIVE 2, S. CEREVISIAE, HOMOLOG OF. [RefSeq;Acc:NM_003350]" UBE2V2
0.239807081 0.847819 1611 0.203313 UTP--GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE 2 (EC 2.7.7.9) (UDP- GLUCOSE PYROPHOSPHORYLASE 2) (UDPGP 2) (UGPASE 2). [SWISSPROT;Acc:Q16851] UGP2
0.239811075 1.24282 1610 0.298042 UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 1 ISOFORM B; DNA-BINDING PROTEIN. [RefSeq;Acc:NM_003349] TMEM189
0.239851847 0.64258 1609 0.154124 KATANIN P60 SUBUNIT A 1. [RefSeq;Acc:NM_007044] KATNA1
0.239865395 0.183648 1608 0.0440508 KATANIN P80 SUBUNIT B 1; KATANIN (80 KDA); KATANIN P80 (WD40-CONTAINING) SUBUNIT B 1. [RefSeq;Acc:NM_005886] KATNB1
0.239870704 0.551914 1607 0.132388 ADENYLYL CYCLASE-ASSOCIATED PROTEIN 2 (CAP 2). [SWISSPROT;Acc:P40123] CAP2
0.239876973 0.967917 1606 0.232181 KATNAL1

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/