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 description Rank measured expected final Hugo
Results: HTML CSV LaTeX Showing element 901 to 950 of 3206 in total
description
Rank
measured
expected
final
Hugo
"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]" 1744 0.357744 1.51127 0.236717463 ATP6V1B2
"VACUOLAR ATP SYNTHASE SUBUNIT B, KIDNEY ISOFORM (EC 3.6.3.14) (V- ATPASE B1 SUBUNIT) (VACUOLAR PROTON PUMP B ISOFORM 1) (ENDOMEMBRANE PROTON PUMP 58 KDA SUBUNIT). [SWISSPROT;Acc:P15313]" 1759 0.299765 1.26636 0.236713889 ATP6V1B1
"ZINC FINGER PROTEIN 289, ID1 REGULATED; LIKELY ORTHOLOG OF MOUSE ZFP289. [RefSeq;Acc:NM_032389]" 489 0.02648 0.0965355 0.274303236 ZNF289
"ZINC RIBBON DOMAIN CONTAINING, 1; TRANSCRIPTION-ASSOCIATED ZINC RIBBON PROTEIN; RNA POLYMERASE I SMALL SPECIFIC SUBUNIT RPA12. [RefSeq;Acc:NM_014596]" 2110 0.193407 0.847287 0.228266219 ZNRD1
"[3-METHYL-2-OXOBUTANOATE DEHYDROGENASE [LIPOAMIDE]] KINASE, MITOCHONDRIAL PRECURSOR (EC 2.7.1.115) (BRANCHED-CHAIN ALPHA-KETOACID DEHYDROGENASE KINASE) (BCKDHKIN) (BCKD-KINASE). [SWISSPROT;Acc:O14874]" 2537 1.13737 5.29857 0.21465603 BCKDK
"[PYRUVATE DEHYDROGENASE [LIPOAMIDE]] KINASE ISOZYME 1, MITOCHONDRIAL PRECURSOR (EC 2.7.1.99) (PYRUVATE DEHYDROGENASE KINASE ISOFORM 1). [SWISSPROT;Acc:Q15118]" 2550 0.844424 3.93515 0.214584959 PDK1
"[PYRUVATE DEHYDROGENASE [LIPOAMIDE]] KINASE ISOZYME 2, MITOCHONDRIAL PRECURSOR (EC 2.7.1.99) (PYRUVATE DEHYDROGENASE KINASE ISOFORM 2). [SWISSPROT;Acc:Q15119]" 2549 0.845658 3.9409 0.214584993 PDK2
1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE ALPHA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 1) (1-AGPAT 1) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-ALPHA) (LPAAT-ALPHA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 1) (G15 PROTEIN). [SWISSPROT;Acc:Q9 2859 0.246538 1.30479 0.188948413 no value
1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE BETA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 2) (1-AGPAT 2) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-BETA) (LPAAT-BETA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 2). [SWISSPROT;Acc:O15120] 2873 0.198456 1.05097 0.18883127 AGPAT2
1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE DELTA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 4) (1-AGPAT 4) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-DELTA) (LPAAT-DELTA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 4). [SWISSPROT;Acc:Q9NRZ5] 2854 0.24139 1.26323 0.191089509 AGPAT4
1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE GAMMA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 3) (1-AGPAT 3) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-GAMMA) (LPAAT-GAMMA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 3). [SWISSPROT;Acc:Q9NRZ7] 2855 0.214138 1.12158 0.190925302 AGPAT3
14-3-3 PROTEIN BETA/ALPHA (PROTEIN KINASE C INHIBITOR PROTEIN-1) (KCIP-1) (PROTEIN 1054). [SWISSPROT;Acc:P31946] 2563 0.286436 1.34026 0.213716742 YWHAB
14-3-3 PROTEIN ZETA/DELTA (PROTEIN KINASE C INHIBITOR PROTEIN-1) (KCIP-1) (FACTOR ACTIVATING EXOENZYME S) (FAS). [SWISSPROT;Acc:P29312] 2576 0.354694 1.66376 0.2131882 YWHAZ
14.5 KDA TRANSLATIONAL INHIBITOR PROTEIN (P14.5) (UK114 ANTIGEN HOMOLOG). [SWISSPROT;Acc:P52758] 2281 0.0509775 0.229168 0.222445978 HRSP12
15 KDA SELENOPROTEIN PRECURSOR. [SWISSPROT;Acc:O60613] 698 0.0424293 0.159817 0.265486775 no value
17 BETA-HYDROXYSTEROID DEHYDROGENASE. [SPTREMBL;Acc:Q13034] 1782 0.024834 0.105517 0.23535544
2-HYDROXYPHYTANOYL-COA LYASE (EC 4.1.-.-) (2-HPCL) (HSPC279). [SWISSPROT;Acc:Q9UJ83] 1491 0.0997445 0.410816 0.242796045 HACL1
20 KDA NUCLEAR CAP BINDING PROTEIN (NCBP 20 KDA SUBUNIT) (CBP20) (NCBP INTERACTING PROTEIN 1) (NIP1). [SWISSPROT;Acc:P52298] 166 0.43784 1.28032 0.341977006 NCBP2
26S PROTEASE REGULATORY SUBUNIT 4 (P26S4). [SWISSPROT;Acc:Q03527] 1872 0.825694 3.54636 0.23282859 PSMC1
26S PROTEASE REGULATORY SUBUNIT 6A (TAT-BINDING PROTEIN 1) (TBP-1) (PROTEASOME SUBUNIT P50). [SWISSPROT;Acc:P17980] 1638 0.766353 3.20427 0.239166175 PSMC3
26S PROTEASE REGULATORY SUBUNIT 6B (MIP224) (MB67 INTERACTING PROTEIN) (TAT-BINDING PROTEIN-7) (TBP-7). [SWISSPROT;Acc:P43686] 1707 0.848985 3.57194 0.237681764 PSMC4
26S PROTEASE REGULATORY SUBUNIT 7 (MSS1 PROTEIN). [SWISSPROT;Acc:P35998] 1709 0.933253 3.92714 0.237641897 PSMC2
26S PROTEASE REGULATORY SUBUNIT 8 (PROTEASOME SUBUNIT P45) (THYROID HORMONE RECEPTOR INTERACTING PROTEIN 1) (TRIP1) (MSUG1 PROTEIN) (TAT-BINDING PROTEIN HOMOLOG 10) (TBP10) (P45/SUG). [SWISSPROT;Acc:P47210] 2062 0.476629 2.07581 0.229611092 PSMC5
26S PROTEASE REGULATORY SUBUNIT S10B (PROTEASOME SUBUNIT P42) (P44) (CONSERVED ATPASE DOMAIN PROTEIN 44) (CADP44). [SWISSPROT;Acc:Q92524] 1614 1.19046 4.96583 0.239730317 PSMC6
26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 1 (26S PROTEASOME REGULATORY SUBUNIT S1) (26S PROTEASOME SUBUNIT P112). [SWISSPROT;Acc:Q99460] 1123 0.263669 1.05182 0.250678823 PSMD1
26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 10 (26S PROTEASOME REGULATORY SUBUNIT P28) (GANKYRIN). [SWISSPROT;Acc:O75832] 1674 0.41158 1.7269 0.238334588 PSMD10
26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 11 (26S PROTEASOME REGULATORY SUBUNIT S9) (26S PROTEASOME REGULATORY SUBUNIT P44.5). [SWISSPROT;Acc:O00231] 1712 0.667497 2.81169 0.237400638 PSMD11
26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 12 (26S PROTEASOME REGULATORY SUBUNIT P55). [SWISSPROT;Acc:O00232] 1680 0.563839 2.36701 0.238207274 no value
26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 13 (26S PROTEASOME REGULATORY SUBUNIT S11) (26S PROTEASOME REGULATORY SUBUNIT P40.5). [SWISSPROT;Acc:Q9UNM6] 1654 0.75685 3.16764 0.238931823 PSMD13
26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 2 (26S PROTEASOME REGULATORY SUBUNIT S2) (26S PROTEASOME SUBUNIT P97) (TUMOR NECROSIS FACTOR TYPE 1 RECEPTOR ASSOCIATED PROTEIN 2) (55.11 PROTEIN). [SWISSPROT;Acc:Q13200] 2164 0.399289 1.75758 0.227181124 PSMD2
26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 3 (26S PROTEASOME REGULATORY SUBUNIT S3) (PROTEASOME SUBUNIT P58). [SWISSPROT;Acc:O43242] 1703 0.779642 3.27908 0.237762421 PSMD3
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] 1644 1.26742 5.30247 0.239024455 PSMD4
26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 6 (26S PROTEASOME REGULATORY SUBUNIT S10) (P42A) (PROTEASOME REGULATORY PARTICLE SUBUNIT P44S10). [SWISSPROT;Acc:Q15008] 1713 0.750885 3.16322 0.237379948 PSMD6
26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 7 (26S PROTEASOME REGULATORY SUBUNIT S12) (PROTEASOME SUBUNIT P40) (MOV34 PROTEIN HOMOLOG). [SWISSPROT;Acc:P51665] 1639 0.790323 3.30538 0.239102009 PSMD7
26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 8 (26S PROTEASOME REGULATORY SUBUNIT S14) (P31). [SWISSPROT;Acc:P48556] 1820 0.824134 3.51793 0.234266742 PSMD8
26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 9 (26S PROTEASOME REGULATORY SUBUNIT P27). [SWISSPROT;Acc:O00233] 1721 0.154828 0.652697 0.237212673 PSMD9
26S PROTEASOME-ASSOCIATED PAD1 HOMOLOG. [RefSeq;Acc:NM_005805] 1389 1.1639 4.76096 0.244467502 PSMD14
27 KDA GOLGI SNARE PROTEIN (GOLGI SNAP RECEPTOR COMPLEX MEMBER 2) (MEMBRIN). [SWISSPROT;Acc:O14653] 806 0.1984 0.757219 0.262011386 GOSR2
3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE (EC 1.1.1.34) (HMG-COA REDUCTASE). [SWISSPROT;Acc:P04035] 2606 0.0963713 0.454692 0.211948528 HMGCR
3-HYDROXYISOBUTYRYL-COENZYME A HYDROLASE. [RefSeq;Acc:NM_014362] 2566 0.512064 2.39827 0.213513908 no value
3-MERCAPTOPYRUVATE SULFURTRANSFERASE (EC 2.8.1.2) (MST). [SWISSPROT;Acc:P25325] 2639 0.0246707 0.117481 0.209997361 MPST
3-OXO-5-ALPHA-STEROID 4-DEHYDROGENASE 1 (EC 1.3.99.5) (STEROID 5-ALPHA-REDUCTASE 1) (SR TYPE 1) (S5AR). [SWISSPROT;Acc:P18405] 1091 0.0411277 0.163477 0.251580956 SRD5A1
3-OXO-5-ALPHA-STEROID 4-DEHYDROGENASE 2 (EC 1.3.99.5) (STEROID 5-ALPHA-REDUCTASE 2) (SR TYPE 2) (5 ALPHA-SR2). [SWISSPROT;Acc:P31213] 1092 0.0324086 0.12882 0.2515805 SRD5A2
3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 (EC 2.7.1.37) (HPDK1). [SWISSPROT;Acc:O15530] 2891 0.61809 3.46554 0.178353157 PDPK1
38 KDA FK-506 BINDING PROTEIN HOMOLOG (FKBPR38) (FK506-BINDING PROTEIN 8). [SWISSPROT;Acc:Q14318] 2916 0.0410645 0.239274 0.171621238 FKBP8
40S RIBOSOMAL PROTEIN S11. [SWISSPROT;Acc:P04643] 1949 0.652807 2.82208 0.231321224 RPS11
40S RIBOSOMAL PROTEIN S13. [SWISSPROT;Acc:Q02546] 1897 0.3472 1.49288 0.232570602 RPS13
40S RIBOSOMAL PROTEIN S14 (PRO2640). [SWISSPROT;Acc:P06366] 1997 0.543161 2.35379 0.230760178 RPS14
40S RIBOSOMAL PROTEIN S15 (RIG PROTEIN). [SWISSPROT;Acc:P11174] 1943 1.32362 5.71513 0.231599281 no value
40S RIBOSOMAL PROTEIN S15A. [SWISSPROT;Acc:P39027] 2059 0.672841 2.92963 0.229667569 RPS15A

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/