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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
measured Gene Rank description expected Hugo final
Results: HTML CSV LaTeX Showing element 2158 to 2207 of 3206 in total
measured
Rank
description
expected
Hugo
final
0.200816 1555 MULTIFUNCTIONAL PROTEIN ADE2 [INCLUDES: PHOSPHORIBOSYLAMINOIMIDAZOLE- SUCCINOCARBOXAMIDE SYNTHASE (EC 6.3.2.6) (SAICAR SYNTHETASE); PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE (EC 4.1.1.21) (AIR CARBOXYLASE) (AIRC)]. [SWISSPROT;Acc:P22234] 0.832 PAICS 0.241365385
0.201117 1310 HUS1 CHECKPOINT PROTEIN; HUS1 (S. POMBE) CHECKPOINT HOMOLOG; HUS1+-LIKE PROTEIN. [RefSeq;Acc:NM_004507] 0.818463 HUS1 0.245725219
0.201492 271 NADH-UBIQUINONE OXIDOREDUCTASE B22 SUBUNIT (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-B22) (CI-B22). [SWISSPROT;Acc:Q9Y6M9] 0.658159 NDUFB9 0.306144868
0.201663 300 "CALPAIN 2, LARGE [CATALYTIC] SUBUNIT PRECURSOR (EC 3.4.22.17) (CALCIUM-ACTIVATED NEUTRAL PROTEINASE) (CANP) (M-TYPE) (M-CALPAIN) (MILLIMOLAR-CALPAIN) (CALPAIN LARGE POLYPEPTIDE L2). [SWISSPROT;Acc:P17655]" 0.672496 CAPN2 0.299872416
0.201803 2898 G2/MITOTIC-SPECIFIC CYCLIN B2. [SWISSPROT;Acc:O95067] 1.15298 CCNB2 0.175027321
0.201833 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]" 0.847008 NONO 0.238289367
0.202064 1193 PROTEASOME SUBUNIT BETA TYPE 6 PRECURSOR (EC 3.4.25.1) (PROTEASOME DELTA CHAIN) (MACROPAIN DELTA CHAIN) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX DELTA CHAIN) (PROTEASOME SUBUNIT Y). [SWISSPROT;Acc:P28072] 0.812918 PSMB6 0.248566276
0.202198 1719 VACUOLAR PROTON TRANSLOCATING ATPASE 116 KDA SUBUNIT A ISOFORM 3 (V- ATPASE 116-KDA ISOFORM A3) (OSTEOCLASTIC PROTON PUMP 116 KDA SUBUNIT) (OC-116 KDA) (OC116) (T-CELL IMMUNE REGULATOR 1) (T CELL IMMUNE RESPONSE CDNA7 PROTEIN) (TIRC7). [SWISSPROT;A 0.852079 TCIRG1 0.237299593
0.20255 658 U2 SMALL NUCLEAR RIBONUCLEOPROTEIN AUXILIARY FACTOR 35 KDA SUBUNIT RELATED-PROTEIN 1. [SWISSPROT;Acc:Q15695] 0.757899 no value 0.267251969
0.203313 1611 UTP--GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE 2 (EC 2.7.7.9) (UDP- GLUCOSE PYROPHOSPHORYLASE 2) (UDPGP 2) (UGPASE 2). [SWISSPROT;Acc:Q16851] 0.847819 UGP2 0.239807081
0.203402 1675 PARASPECKLE PROTEIN 1. [RefSeq;Acc:NM_018282] 0.853581 PSPC1 0.238292558
0.203468 2683 RETICULON PROTEIN 3 (NEUROENDOCRINE-SPECIFIC PROTEIN-LIKE 2) (NSP-LIKE PROTEIN II) (NSPLII). [SWISSPROT;Acc:O95197] 0.976589 RTN3 0.208345578
0.203633 45 GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE PROTEIN GADD45 GAMMA (CYTOKINE RESPONSIVE PROTEIN CR6). [SWISSPROT;Acc:O95257] 0.488304 GADD45G 0.417020954
0.204254 3051 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(T) BETA SUBUNIT 1 (TRANSDUCIN BETA CHAIN 1). [SWISSPROT;Acc:P04901] 1.92471 GNB1 0.106121961
0.204288 3062 "T-COMPLEX PROTEIN 1, EPSILON SUBUNIT (TCP-1-EPSILON) (CCT-EPSILON). [SWISSPROT;Acc:P48643]" 1.93831 CCT5 0.105394906
0.204365 83 TRANSCRIPTION FACTOR E2F2 (E2F-2). [SWISSPROT;Acc:Q14209] 0.519607 E2F2 0.393306865
0.204901 649 RETINOIC ACID INDUCED 17; PIAS-LIKE PROTEIN HZIMP10. [RefSeq;Acc:NM_020338] 0.765015 ZMIZ1 0.267839193
0.205001 2477 SIMILAR TO TRNA SYNTHETASE CLASS II. [RefSeq;Acc:NM_152268] 0.946559 PARS2 0.216574984
0.205566 156 0.585616 DTX4 0.351025245
0.205623 301 "CALPAIN 1, LARGE [CATALYTIC] SUBUNIT (EC 3.4.22.17) (CALCIUM-ACTIVATED NEUTRAL PROTEINASE) (CANP) (MU-TYPE) (MUCANP) (MICROMOLAR-CALPAIN). [SWISSPROT;Acc:P07384]" 0.685711 CAPN1 0.299868312
0.205647 2448 CAAX PRENYL PROTEASE 1 HOMOLOG (EC 3.4.24.-) (PRENYL PROTEIN-SPECIFIC ENDOPROTEASE 1) (FARNESYLATED-PROTEINS CONVERTING ENZYME 1) (FACE-1) (ZINC METALLOPROTEINASE STE24 HOMOLOG). [SWISSPROT;Acc:O75844] 0.94731 ZMPSTE24 0.21708522
0.205692 1280 CALRETICULIN PRECURSOR (CRP55) (CALREGULIN) (HACBP) (ERP60). [SWISSPROT;Acc:P27797] 0.834998 CALR 0.246338315
0.206188 3000 APG3P; PC3-96 PROTEIN. [RefSeq;Acc:NM_022488] 1.59883 ATG3 0.128961803
0.206261 782 SYNTAXIN 12. [RefSeq;Acc:NM_177424] 0.78389 STX12 0.263124928
0.206722 2381 0.940952 USP52 0.219694522
0.207889 2180 "GLYCINE CLEAVAGE SYSTEM H PROTEIN, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:P23434]" 0.916816 no value 0.22675106
0.208436 922 ALPHA CRYSTALLIN C CHAIN (SMALL STRESS PROTEIN-LIKE PROTEIN HSP22) (E2IG1) (PROTEIN KINASE H11). [SWISSPROT;Acc:Q9UJY1] 0.808729 HSPB8 0.257732813
0.20849 303 HPAII TINY FRAGMENTS LOCUS 9C. [RefSeq;Acc:NM_022727] 0.697153 no value 0.299059174
0.208499 1765 GLUTATHIONE S-TRANSFERASE P (EC 2.5.1.18) (GST CLASS-PI) (GSTP1-1). [SWISSPROT;Acc:P09211] 0.882968 GSTP1 0.236134265
0.208649 2500 "MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 3.4.24.64) (BETA-MPP) (P-52). [SWISSPROT;Acc:O75439]" 0.969013 PMPCB 0.215321157
0.208679 2310 0.939792 DCAKD 0.22204807
0.209001 642 "TRANSCRIPTION FACTOR CP2; TRANSCRIPTION FACTOR CP2, ALPHA GLOBIN. [RefSeq;Acc:NM_005653]" 0.779209 TFCP2 0.268222005
0.209195 480 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 7 (EC 2.7.1.-) (MAP KINASE KINASE 7) (MAPKK 7) (MAPK/ERK KINASE 7) (JNK ACTIVATING KINASE 2) (C-JUN N-TERMINAL KINASE KINASE 2) (JNK KINASE 2) (JNKK 2). [SWISSPROT;Acc:O14733] 0.762639 MAP2K7 0.274304094
0.209282 786 SYNTAXIN 7. [SWISSPROT;Acc:O15400] 0.797115 STX7 0.262549318
0.209882 955 VACUOLAR PROTEIN SORTING 16 (HVPS16). [SWISSPROT;Acc:Q9H269] 0.818777 PTPRA 0.256335974
0.210207 1701 NEMO-LIKE KINASE; LIKELY ORTHOLOG OF MOUSE NEMO LIKE KINASE. [RefSeq;Acc:NM_016231] 0.883788 NLK 0.237847764
0.210228 2465 0.970087 BRD9 0.21671046
0.210608 2946 PROTEASOME SUBUNIT ALPHA TYPE 5 (EC 3.4.25.1) (PROTEASOME ZETA CHAIN) (MACROPAIN ZETA CHAIN) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX ZETA CHAIN). [SWISSPROT;Acc:P28066] 1.38339 PSMA5 0.152240511
0.210706 1627 "CAMP-DEPENDENT PROTEIN KINASE, BETA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-BETA). [SWISSPROT;Acc:P22694]" 0.880269 PRKACB 0.239365467
1628 "CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-ALPHA). [SWISSPROT;Acc:P17612]" PRKACA
0.210781 253 DI-RAS2. [RefSeq;Acc:NM_017594] 0.675823 DIRAS2 0.311887876
0.210907 1596 LAMIN B1. [SWISSPROT;Acc:P20700] 0.877854 LMNB1 0.240252935
0.211371 143 GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-1 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P14867] 0.601543 GABRA1 0.351381364
0.211718 144 GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-2 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P47869] 0.602532 GABRA2 0.351380508
0.211834 1718 VACUOLAR PROTON TRANSLOCATING ATPASE 116 KDA SUBUNIT A ISOFORM 2 (V-ATPASE 116-KDA ISOFORM A2) (TJ6). [SWISSPROT;Acc:Q9Y487] 0.892673 ATP6V0A2 0.237303021
0.211877 1006 ORPHAN NUCLEAR RECEPTOR TR2. [SWISSPROT;Acc:P13056] 0.831867 NR2C1 0.254700571
0.2125 141 GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-3 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P34903] 0.604755 GABRA3 0.351381965
0.212647 76 0.523598 C22orf9 0.406126456
0.212723 416 CLATHRIN COAT ASSEMBLY PROTEIN AP180 (CLATHRIN COAT ASSOCIATED PROTEIN AP180) (91 KDA SYNAPTOSOMAL-ASSOCIATED PROTEIN). [SWISSPROT;Acc:O60641] 0.766919 SNAP91 0.277373491
0.212972 1946 PRE-MRNA CLEAVAGE COMPLEX II PROTEIN CLP1. [SWISSPROT;Acc:Q92989] 0.920283 CLP1 0.231420118

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/