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 [...,...].
Rank Gene description measured expected Hugo final
Results: HTML CSV LaTeX Showing element 2102 to 2151 of 3206 in total
Rank
description
measured
expected
Hugo
final
2102 0.0653467 0.286165 INTS8 0.228353223
2103 0.0653647 0.286244 GON4L 0.228353083
2104 "PROTEIN KINASE C, EPSILON TYPE (EC 2.7.1.-) (NPKC-EPSILON). [SWISSPROT;Acc:Q02156]" PRKCE
2105 UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANSFERASE 110 KDA SUBUNIT (EC 2.4.1.-) (O-GLCNAC TRANSFERASE P110 SUBUNIT). [SWISSPROT;Acc:O15294] 0.173405 0.759373 OGT 0.228352865
2106 "PROTEIN KINASE C, ETA TYPE (EC 2.7.1.-) (NPKC-ETA) (PKC-L). [SWISSPROT;Acc:P24723]" 0.0507599 0.222289 PRKCH 0.228350931
2107 0.0325606 0.142608 FBXO42 0.228322394
2108 0.0651212 0.285217 PUS7 0.228321594
2109 TUBULIN-TYROSINE LIGASE. [RefSeq;Acc:NM_153712] 0.130242 0.570434 TTL 0.228320893
2110 "ZINC RIBBON DOMAIN CONTAINING, 1; TRANSCRIPTION-ASSOCIATED ZINC RIBBON PROTEIN; RNA POLYMERASE I SMALL SPECIFIC SUBUNIT RPA12. [RefSeq;Acc:NM_014596]" 0.193407 0.847287 ZNRD1 0.228266219
2111 SIGNAL TRANSDUCING ADAPTOR MOLECULE 1; SIGNAL TRANSDUCING ADAPTOR MOLECULE. [RefSeq;Acc:NM_003473] 0.405058 1.77451 STAM 0.228264704
2112 0.0298356 0.130757 DPY19L2 0.228175929
2113 "ORNITHINE AMINOTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.6.1.13) (ORNITHINE--OXO-ACID AMINOTRANSFERASE). [SWISSPROT;Acc:P04181]" 0.0906856 0.397439 OAT 0.22817489
2114 SPHINGOSINE-1-PHOSPHATE LYASE 1; SPHINGOSINE-1-PHOSPHATE LYASE. [RefSeq;Acc:NM_003901] 0.0601623 0.263668 SGPL1 0.228174447
2115 "4-AMINOBUTYRATE AMINOTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.6.1.19) (GAMMA-AMINO-N-BUTYRATE TRANSAMINASE) (GABA TRANSAMINASE) (GABA AMINOTRANSFERASE) (GABA-AT) (GABA-T). [SWISSPROT;Acc:P80404]" 0.16968 0.743642 no value 0.22817431
2116 0.0243642 0.106779 DPY19L2P2 0.228174079
2117 HYDROXYINDOLE O-METHYLTRANSFERASE (EC 2.1.1.4) (HIOMT) (ACETYLSEROTONIN O-METHYLTRANSFERASE) (ASMT). [SWISSPROT;Acc:P46597] 0.253802 1.11232 no value 0.228173547
2118 0.0256791 0.112542 DPY19L1 0.228173482
2119 "PEROXISOMAL 3,2-TRANS-ENOYL-COA ISOMERASE (EC 5.3.3.8) (DODECENOYL-COA DELTA-ISOMERASE) (D3,D2-ENOYL-COA ISOMERASE) (DBI-RELATED PROTEIN 1) (DRS-1) (HEPATOCELLULAR CARCINOMA-ASSOCIATED ANTIGEN 88). [SWISSPROT;Acc:O75521]" 0.745512 3.26763 no value 0.228150678
2120 TUBULIN GAMMA-1 CHAIN (GAMMA-1 TUBULIN) (GAMMA-TUBULIN COMPLEX COMPONENT 1) (GCP-1). [SWISSPROT;Acc:P23258] 0.123817 0.542764 TUBG1 0.228123088
2121 "LIPOATE-PROTEIN LIGASE, MITOCHONDRIAL PRECURSOR (EC 6.-.-.-) (LIPOATE BIOSYNTHESIS PROTEIN) (LIPOYL LIGASE) (LIPOYLTRANSFERASE). [SWISSPROT;Acc:Q9Y234]" 0.391899 1.71793 LIPT1 0.228122799
2122 DEFENDER AGAINST CELL DEATH 1 (DAD-1). [SWISSPROT;Acc:P46966] 0.0621814 0.272579 DAD1 0.228122489
2123 0.0476698 0.208966 TCP11L2 0.228122278
2124 T-COMPLEX 11. [RefSeq;Acc:NM_018679] 0.0342505 0.150141 TCP11 0.228122232
2125 0.038682 0.169567 TCP11L1 0.228122217
2126 TUBULIN GAMMA-2 CHAIN (GAMMA-2 TUBULIN). [SWISSPROT;Acc:Q9NRH3] 0.121148 0.531068 TUBG2 0.228121446
2127 "GLYCINE DEHYDROGENASE [DECARBOXYLATING], MITOCHONDRIAL PRECURSOR (EC 1.4.4.2) (GLYCINE DECARBOXYLASE) (GLYCINE CLEAVAGE SYSTEM P- PROTEIN). [SWISSPROT;Acc:P23378]" 0.0640341 0.280704 no value 0.228119656
2128 "CLEAVAGE STIMULATION FACTOR, 64 KDA SUBUNIT (CSTF 64 KDA SUBUNIT) (CF-1 64 KDA SUBUNIT). [SWISSPROT;Acc:P33240]" 0.386793 1.69586 CSTF2 0.228080738
2129 BA207C16.2 (FRAGMENT). [SPTREMBL;Acc:Q9NQL7] 0.214415 0.940372 KIAA1432 0.22801083
2130 "RUNT-RELATED TRANSCRIPTION FACTOR 2 (CORE-BINDING FACTOR, ALPHA 1 SUBUNIT) (CBF-ALPHA 1) (ACUTE MYELOID LEUKEMIA 3 PROTEIN) (ONCOGENE AML-3) (POLYOMAVIRUS ENHANCER BINDING PROTEIN 2 ALPHA A SUBUNIT) (PEBP2-ALPHA A) (PEA2-ALPHA A) (SL3-3 ENHANCER FACTOR 1 " 0.0548378 0.24054 RUNX2 0.227977883
2131 NEUROPILIN- AND TOLLOID-LIKE PROTEIN 2 PRECURSOR. [RefSeq;Acc:NM_018092] NETO2
2132 60S RIBOSOMAL PROTEIN L18. [SWISSPROT;Acc:Q07020] 0.35482 1.55638 RPL18 0.227977743
2133 E1B-55KDA-ASSOCIATED PROTEIN 5 ISOFORM A. [RefSeq;Acc:NM_007040] 0.0829182 0.363712 HNRPUL1 0.227977631
2134 NEUROPILIN- AND TOLLOID-LIKE PROTEIN 1 ISOFORM 3 PRECURSOR. [RefSeq;Acc:NM_138966] 0.046465 0.203814 NETO1 0.22797747
2135 HETEROGENOUS NUCLEAR RIBONUCLEOPROTEIN U (HNRNP U) (SCAFFOLD ATTACHMENT FACTOR A) (SAF-A). [SWISSPROT;Acc:Q00839] 0.0651336 0.285702 HNRNPU 0.227977403
2136 0.0629265 0.276021 BSCL2 0.227977219
2137 TRANSALDOLASE (EC 2.2.1.2). [SWISSPROT;Acc:P37837] 0.0846644 0.371472 TALDO1 0.227915967
2138 CD109; GOV SYSTEM ALLOANTIGENS ON PLATELETS. [RefSeq;Acc:NM_133493] 0.0227421 0.0998232 CD109 0.227823792
2139 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1 (EC 5.2.1.8) (ROTAMASE PIN1) (PPIASE PIN1). [SWISSPROT;Acc:Q13526] 0.347798 1.52661 PIN1 0.22782374
2140 0.0510195 0.223943 KIAA1109 0.227823598
2141 0.0218584 0.0959445 ZC3H12C 0.227823377
2142 IROQUOIS-CLASS HOMEODOMAIN PROTEIN IRX-4 (IROQUOIS HOMEOBOX PROTEIN 4). [SWISSPROT;Acc:P78413] 0.0282774 0.12412 IRX4 0.227823074
2143 ZC3H12A
2144 IMMATURE COLON CARCINOMA TRANSCRIPT 1 (DIGESTION SUBSTRACTION 1) (DS- 1). [SWISSPROT;Acc:Q14197] 0.221521 0.972411 ICT1 0.227805938
2145 ANAPHASE PROMOTING COMPLEX SUBUNIT 11 (HEPATOCELLULAR CARCINOMA ASSOCIATED RING FINGER PROTEIN) (HSPC214). [SWISSPROT;Acc:Q9NYG5] 0.170664 0.749796 ANAPC11 0.227613911
2146 "MMS19-LIKE (MET18 HOMOLOG, S. CEREVISIAE); HOMOLOG OF YEAST MMS19; MMS19 (MET18 S. CEREVISIAE)-LIKE. [RefSeq;Acc:NM_022362]" 0.155283 0.682226 MMS19 0.227612258
2147 TRANSLATIONALLY CONTROLLED TUMOR PROTEIN (TCTP) (P23) (HISTAMINE- RELEASING FACTOR) (HRF). [SWISSPROT;Acc:P13693] 0.06101 0.268263 TPT1 0.227426071
2148 APOPTOSIS INHIBITOR FKSG2. [SWISSPROT;Acc:Q9HAU6] 0.0544712 0.239562 no value 0.227378299
2149 C18B11 HOMOLOG (44.9KD). [RefSeq;Acc:NM_152260] 0.481419 2.11777 RPUSD2 0.227323553
2150 LIFEGUARD; KIAA0950 PROTEIN. [RefSeq;Acc:NM_012306] 0.0891166 0.392026 FAIM2 0.227323188
2151 STEROL REGULATORY ELEMENT BINDING PROTEIN-2 (SREBP-2) (STEROL REGULATORY ELEMENT-BINDING TRANSCRIPTION FACTOR 2). [SWISSPROT;Acc:Q12772] 0.0569865 0.250685 no value 0.227323135

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/