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 final Hugo
Results: HTML CSV LaTeX Showing element 2102 to 2151 of 3206 in total
Rank
description
measured
expected
final
Hugo
2102 0.0653467 0.286165 0.228353223 INTS8
2103 0.0653647 0.286244 0.228353083 GON4L
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 0.228352865 OGT
2106 "PROTEIN KINASE C, ETA TYPE (EC 2.7.1.-) (NPKC-ETA) (PKC-L). [SWISSPROT;Acc:P24723]" 0.0507599 0.222289 0.228350931 PRKCH
2107 0.0325606 0.142608 0.228322394 FBXO42
2108 0.0651212 0.285217 0.228321594 PUS7
2109 TUBULIN-TYROSINE LIGASE. [RefSeq;Acc:NM_153712] 0.130242 0.570434 0.228320893 TTL
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 0.228266219 ZNRD1
2111 SIGNAL TRANSDUCING ADAPTOR MOLECULE 1; SIGNAL TRANSDUCING ADAPTOR MOLECULE. [RefSeq;Acc:NM_003473] 0.405058 1.77451 0.228264704 STAM
2112 0.0298356 0.130757 0.228175929 DPY19L2
2113 "ORNITHINE AMINOTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.6.1.13) (ORNITHINE--OXO-ACID AMINOTRANSFERASE). [SWISSPROT;Acc:P04181]" 0.0906856 0.397439 0.22817489 OAT
2114 SPHINGOSINE-1-PHOSPHATE LYASE 1; SPHINGOSINE-1-PHOSPHATE LYASE. [RefSeq;Acc:NM_003901] 0.0601623 0.263668 0.228174447 SGPL1
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 0.22817431 no value
2116 0.0243642 0.106779 0.228174079 DPY19L2P2
2117 HYDROXYINDOLE O-METHYLTRANSFERASE (EC 2.1.1.4) (HIOMT) (ACETYLSEROTONIN O-METHYLTRANSFERASE) (ASMT). [SWISSPROT;Acc:P46597] 0.253802 1.11232 0.228173547 no value
2118 0.0256791 0.112542 0.228173482 DPY19L1
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 0.228150678 no value
2120 TUBULIN GAMMA-1 CHAIN (GAMMA-1 TUBULIN) (GAMMA-TUBULIN COMPLEX COMPONENT 1) (GCP-1). [SWISSPROT;Acc:P23258] 0.123817 0.542764 0.228123088 TUBG1
2121 "LIPOATE-PROTEIN LIGASE, MITOCHONDRIAL PRECURSOR (EC 6.-.-.-) (LIPOATE BIOSYNTHESIS PROTEIN) (LIPOYL LIGASE) (LIPOYLTRANSFERASE). [SWISSPROT;Acc:Q9Y234]" 0.391899 1.71793 0.228122799 LIPT1
2122 DEFENDER AGAINST CELL DEATH 1 (DAD-1). [SWISSPROT;Acc:P46966] 0.0621814 0.272579 0.228122489 DAD1
2123 0.0476698 0.208966 0.228122278 TCP11L2
2124 T-COMPLEX 11. [RefSeq;Acc:NM_018679] 0.0342505 0.150141 0.228122232 TCP11
2125 0.038682 0.169567 0.228122217 TCP11L1
2126 TUBULIN GAMMA-2 CHAIN (GAMMA-2 TUBULIN). [SWISSPROT;Acc:Q9NRH3] 0.121148 0.531068 0.228121446 TUBG2
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 0.228119656 no value
2128 "CLEAVAGE STIMULATION FACTOR, 64 KDA SUBUNIT (CSTF 64 KDA SUBUNIT) (CF-1 64 KDA SUBUNIT). [SWISSPROT;Acc:P33240]" 0.386793 1.69586 0.228080738 CSTF2
2129 BA207C16.2 (FRAGMENT). [SPTREMBL;Acc:Q9NQL7] 0.214415 0.940372 0.22801083 KIAA1432
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 0.227977883 RUNX2
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 0.227977743 RPL18
2133 E1B-55KDA-ASSOCIATED PROTEIN 5 ISOFORM A. [RefSeq;Acc:NM_007040] 0.0829182 0.363712 0.227977631 HNRPUL1
2134 NEUROPILIN- AND TOLLOID-LIKE PROTEIN 1 ISOFORM 3 PRECURSOR. [RefSeq;Acc:NM_138966] 0.046465 0.203814 0.22797747 NETO1
2135 HETEROGENOUS NUCLEAR RIBONUCLEOPROTEIN U (HNRNP U) (SCAFFOLD ATTACHMENT FACTOR A) (SAF-A). [SWISSPROT;Acc:Q00839] 0.0651336 0.285702 0.227977403 HNRNPU
2136 0.0629265 0.276021 0.227977219 BSCL2
2137 TRANSALDOLASE (EC 2.2.1.2). [SWISSPROT;Acc:P37837] 0.0846644 0.371472 0.227915967 TALDO1
2138 CD109; GOV SYSTEM ALLOANTIGENS ON PLATELETS. [RefSeq;Acc:NM_133493] 0.0227421 0.0998232 0.227823792 CD109
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 0.22782374 PIN1
2140 0.0510195 0.223943 0.227823598 KIAA1109
2141 0.0218584 0.0959445 0.227823377 ZC3H12C
2142 IROQUOIS-CLASS HOMEODOMAIN PROTEIN IRX-4 (IROQUOIS HOMEOBOX PROTEIN 4). [SWISSPROT;Acc:P78413] 0.0282774 0.12412 0.227823074 IRX4
2143 ZC3H12A
2144 IMMATURE COLON CARCINOMA TRANSCRIPT 1 (DIGESTION SUBSTRACTION 1) (DS- 1). [SWISSPROT;Acc:Q14197] 0.221521 0.972411 0.227805938 ICT1
2145 ANAPHASE PROMOTING COMPLEX SUBUNIT 11 (HEPATOCELLULAR CARCINOMA ASSOCIATED RING FINGER PROTEIN) (HSPC214). [SWISSPROT;Acc:Q9NYG5] 0.170664 0.749796 0.227613911 ANAPC11
2146 "MMS19-LIKE (MET18 HOMOLOG, S. CEREVISIAE); HOMOLOG OF YEAST MMS19; MMS19 (MET18 S. CEREVISIAE)-LIKE. [RefSeq;Acc:NM_022362]" 0.155283 0.682226 0.227612258 MMS19
2147 TRANSLATIONALLY CONTROLLED TUMOR PROTEIN (TCTP) (P23) (HISTAMINE- RELEASING FACTOR) (HRF). [SWISSPROT;Acc:P13693] 0.06101 0.268263 0.227426071 TPT1
2148 APOPTOSIS INHIBITOR FKSG2. [SWISSPROT;Acc:Q9HAU6] 0.0544712 0.239562 0.227378299 no value
2149 C18B11 HOMOLOG (44.9KD). [RefSeq;Acc:NM_152260] 0.481419 2.11777 0.227323553 RPUSD2
2150 LIFEGUARD; KIAA0950 PROTEIN. [RefSeq;Acc:NM_012306] 0.0891166 0.392026 0.227323188 FAIM2
2151 STEROL REGULATORY ELEMENT BINDING PROTEIN-2 (SREBP-2) (STEROL REGULATORY ELEMENT-BINDING TRANSCRIPTION FACTOR 2). [SWISSPROT;Acc:Q12772] 0.0569865 0.250685 0.227323135 no value

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/