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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Rank Gene description measured Hugo expected final
Results: HTML CSV LaTeX Showing element 2108 to 2157 of 3206 in total
Rank
description
measured
Hugo
expected
final
2108 0.0651212 PUS7 0.285217 0.228321594
2109 TUBULIN-TYROSINE LIGASE. [RefSeq;Acc:NM_153712] 0.130242 TTL 0.570434 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 ZNRD1 0.847287 0.228266219
2111 SIGNAL TRANSDUCING ADAPTOR MOLECULE 1; SIGNAL TRANSDUCING ADAPTOR MOLECULE. [RefSeq;Acc:NM_003473] 0.405058 STAM 1.77451 0.228264704
2112 0.0298356 DPY19L2 0.130757 0.228175929
2113 "ORNITHINE AMINOTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.6.1.13) (ORNITHINE--OXO-ACID AMINOTRANSFERASE). [SWISSPROT;Acc:P04181]" 0.0906856 OAT 0.397439 0.22817489
2114 SPHINGOSINE-1-PHOSPHATE LYASE 1; SPHINGOSINE-1-PHOSPHATE LYASE. [RefSeq;Acc:NM_003901] 0.0601623 SGPL1 0.263668 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 no value 0.743642 0.22817431
2116 0.0243642 DPY19L2P2 0.106779 0.228174079
2117 HYDROXYINDOLE O-METHYLTRANSFERASE (EC 2.1.1.4) (HIOMT) (ACETYLSEROTONIN O-METHYLTRANSFERASE) (ASMT). [SWISSPROT;Acc:P46597] 0.253802 no value 1.11232 0.228173547
2118 0.0256791 DPY19L1 0.112542 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 no value 3.26763 0.228150678
2120 TUBULIN GAMMA-1 CHAIN (GAMMA-1 TUBULIN) (GAMMA-TUBULIN COMPLEX COMPONENT 1) (GCP-1). [SWISSPROT;Acc:P23258] 0.123817 TUBG1 0.542764 0.228123088
2121 "LIPOATE-PROTEIN LIGASE, MITOCHONDRIAL PRECURSOR (EC 6.-.-.-) (LIPOATE BIOSYNTHESIS PROTEIN) (LIPOYL LIGASE) (LIPOYLTRANSFERASE). [SWISSPROT;Acc:Q9Y234]" 0.391899 LIPT1 1.71793 0.228122799
2122 DEFENDER AGAINST CELL DEATH 1 (DAD-1). [SWISSPROT;Acc:P46966] 0.0621814 DAD1 0.272579 0.228122489
2123 0.0476698 TCP11L2 0.208966 0.228122278
2124 T-COMPLEX 11. [RefSeq;Acc:NM_018679] 0.0342505 TCP11 0.150141 0.228122232
2125 0.038682 TCP11L1 0.169567 0.228122217
2126 TUBULIN GAMMA-2 CHAIN (GAMMA-2 TUBULIN). [SWISSPROT;Acc:Q9NRH3] 0.121148 TUBG2 0.531068 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 no value 0.280704 0.228119656
2128 "CLEAVAGE STIMULATION FACTOR, 64 KDA SUBUNIT (CSTF 64 KDA SUBUNIT) (CF-1 64 KDA SUBUNIT). [SWISSPROT;Acc:P33240]" 0.386793 CSTF2 1.69586 0.228080738
2129 BA207C16.2 (FRAGMENT). [SPTREMBL;Acc:Q9NQL7] 0.214415 KIAA1432 0.940372 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 RUNX2 0.24054 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 RPL18 1.55638 0.227977743
2133 E1B-55KDA-ASSOCIATED PROTEIN 5 ISOFORM A. [RefSeq;Acc:NM_007040] 0.0829182 HNRPUL1 0.363712 0.227977631
2134 NEUROPILIN- AND TOLLOID-LIKE PROTEIN 1 ISOFORM 3 PRECURSOR. [RefSeq;Acc:NM_138966] 0.046465 NETO1 0.203814 0.22797747
2135 HETEROGENOUS NUCLEAR RIBONUCLEOPROTEIN U (HNRNP U) (SCAFFOLD ATTACHMENT FACTOR A) (SAF-A). [SWISSPROT;Acc:Q00839] 0.0651336 HNRNPU 0.285702 0.227977403
2136 0.0629265 BSCL2 0.276021 0.227977219
2137 TRANSALDOLASE (EC 2.2.1.2). [SWISSPROT;Acc:P37837] 0.0846644 TALDO1 0.371472 0.227915967
2138 CD109; GOV SYSTEM ALLOANTIGENS ON PLATELETS. [RefSeq;Acc:NM_133493] 0.0227421 CD109 0.0998232 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 PIN1 1.52661 0.22782374
2140 0.0510195 KIAA1109 0.223943 0.227823598
2141 0.0218584 ZC3H12C 0.0959445 0.227823377
2142 IROQUOIS-CLASS HOMEODOMAIN PROTEIN IRX-4 (IROQUOIS HOMEOBOX PROTEIN 4). [SWISSPROT;Acc:P78413] 0.0282774 IRX4 0.12412 0.227823074
2143 ZC3H12A
2144 IMMATURE COLON CARCINOMA TRANSCRIPT 1 (DIGESTION SUBSTRACTION 1) (DS- 1). [SWISSPROT;Acc:Q14197] 0.221521 ICT1 0.972411 0.227805938
2145 ANAPHASE PROMOTING COMPLEX SUBUNIT 11 (HEPATOCELLULAR CARCINOMA ASSOCIATED RING FINGER PROTEIN) (HSPC214). [SWISSPROT;Acc:Q9NYG5] 0.170664 ANAPC11 0.749796 0.227613911
2146 "MMS19-LIKE (MET18 HOMOLOG, S. CEREVISIAE); HOMOLOG OF YEAST MMS19; MMS19 (MET18 S. CEREVISIAE)-LIKE. [RefSeq;Acc:NM_022362]" 0.155283 MMS19 0.682226 0.227612258
2147 TRANSLATIONALLY CONTROLLED TUMOR PROTEIN (TCTP) (P23) (HISTAMINE- RELEASING FACTOR) (HRF). [SWISSPROT;Acc:P13693] 0.06101 TPT1 0.268263 0.227426071
2148 APOPTOSIS INHIBITOR FKSG2. [SWISSPROT;Acc:Q9HAU6] 0.0544712 no value 0.239562 0.227378299
2149 C18B11 HOMOLOG (44.9KD). [RefSeq;Acc:NM_152260] 0.481419 RPUSD2 2.11777 0.227323553
2150 LIFEGUARD; KIAA0950 PROTEIN. [RefSeq;Acc:NM_012306] 0.0891166 FAIM2 0.392026 0.227323188
2151 STEROL REGULATORY ELEMENT BINDING PROTEIN-2 (SREBP-2) (STEROL REGULATORY ELEMENT-BINDING TRANSCRIPTION FACTOR 2). [SWISSPROT;Acc:Q12772] 0.0569865 no value 0.250685 0.227323135
2152 PP1201 PROTEIN. [RefSeq;Acc:NM_022152] 0.0628846 TMBIM1 0.276631 0.22732304
2153 STEROL REGULATORY ELEMENT BINDING PROTEIN-1 (SREBP-1) (STEROL REGULATORY ELEMENT-BINDING TRANSCRIPTION FACTOR 1). [SWISSPROT;Acc:P36956] 0.0687827 SREBF1 0.302577 0.227322962
2154 Z-PROTEIN (PROTEIN CGI-119) (S1R PROTEIN). [SWISSPROT;Acc:Q9HC24] 0.0343914 TMBIM4 0.151289 0.227322542
2155 LEUCYL-TRNA SYNTHETASE. [RefSeq;Acc:NM_020117] 0.159792 LARS 0.703125 0.227259733
2156 "PROBABLE LEUCYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.4) (LEUCINE--TRNA LIGASE) (LEURS). [SWISSPROT;Acc:Q15031]" 0.159922 LARS2 0.7037 0.227258775
2157 0.0141571 BPIL2 0.0622988 0.227245148

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/