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 expected final Hugo
Results: HTML CSV LaTeX Showing element 1051 to 1100 of 3206 in total
Rank
description
measured
expected
final
Hugo
1051 RNA (GUANINE-7-) METHYLTRANSFERASE. [RefSeq;Acc:NM_003799] 0.0429379 0.169867 0.252773641 RNMT
1052 ANNEXIN A7 (ANNEXIN VII) (SYNEXIN). [SWISSPROT;Acc:P20073] 0.149169 0.590289 0.252705031 ANXA7
1053 CLATHRIN HEAVY CHAIN 1 (CLH-17). [SWISSPROT;Acc:Q00610] 0.264806 1.04802 0.252672659 CLTC
1054 PHOSDUCIN-LIKE PROTEIN (PHLP). [SWISSPROT;Acc:Q13371] 0.0344183 0.136218 0.252670719 PDCL
1055 DNA REPAIR PROTEIN RAD52 HOMOLOG. [SWISSPROT;Acc:P43351] RAD52
1056 REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT (RP-A) (RF-A) (REPLICATION FACTOR-A PROTEIN 1) (SINGLE-STRANDED DNA-BINDING PROTEIN). [SWISSPROT;Acc:P27694] 0.0688366 0.272436 RPA1
1057 REPLICATION PROTEIN A 32 KDA SUBUNIT (RP-A) (RF-A) (REPLICATION FACTOR-A PROTEIN 2). [SWISSPROT;Acc:P15927] 0.160828 0.636513 0.252670409 RPA2
1058 PHOSDUCIN (PHD) (33 KDA PHOTOTRANSDUCING PROTEIN) (MEKA PROTEIN). [SWISSPROT;Acc:P20941] 0.0280767 0.11112 0.252670086 PDC
1059 CLATHRIN HEAVY CHAIN 2 (CLH-22). [SWISSPROT;Acc:P53675] 0.225517 0.892542 0.252668222 CLTCL1
1060 GERM CELL-LESS. [RefSeq;Acc:NM_022471] 0.398407 1.57699 0.25263762 no value
1061 PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR-2 (HOMEOBOX PROTEIN PBX2) (G17 PROTEIN). [SWISSPROT;Acc:P40425] 0.294647 1.16629 0.252636137
1062 PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR 4. [RefSeq;Acc:NM_025245] 0.122601 0.485287 0.252636069 PBX4
1063 PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR-3 (HOMEOBOX PROTEIN PBX3). [SWISSPROT;Acc:P40426] 0.283637 1.12271 0.252636032 PBX3
1064 BAG-FAMILY MOLECULAR CHAPERONE REGULATOR-2. [SWISSPROT;Acc:O95816] 0.15369 0.608346 0.252635836 BAG2
1065 HYPORTHETICAL PROTEIN MGC27169. [RefSeq;Acc:NM_176782] 0.118754 0.47006 0.252635834 C1orf179
1066 HOMEOBOX PROTEIN MEIS3 (MEIS1-RELATED PROTEIN 2) (FRAGMENT). [SWISSPROT;Acc:Q99687] 0.285122 1.12859 0.25263559 MEIS3
1067 HOMEOBOX PROTEIN MEIS1. [SWISSPROT;Acc:O00470] 0.352414 1.39495 0.252635578 MEIS1
1068 HOMEOBOX PROTEIN MEIS2 (MEIS1-RELATED PROTEIN 1). [SWISSPROT;Acc:O14770] 0.322799 1.27773 0.252634751 MEIS2
1069 PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR-1 (HOMEOBOX PROTEIN PBX1) (HOMEOBOX PROTEIN PRL). [SWISSPROT;Acc:P40424] 0.301322 1.19272 0.252634315 PBX1
1070 0.412942 1.63455 0.252633447 GMCL1
1071 PROTEASOME SUBUNIT BETA TYPE 10 PRECURSOR (EC 3.4.25.1) (PROTEASOME MECL-1) (MACROPAIN SUBUNIT MECL-1) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT MECL-1). [SWISSPROT;Acc:P40306] 0.0742909 0.294313 0.252421402 CTRL
1072 IMPORTIN-ALPHA RE-EXPORTER (CHROMOSOME SEGREGATION 1-LIKE PROTEIN) (CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN). [SWISSPROT;Acc:P55060] 0.0342868 0.135906 0.252283196 CSE1L
1073 0.832577 3.30018 0.2522823 EIF2AK4
1074 JUNCTION PLAKOGLOBIN (DESMOPLAKIN III). [SWISSPROT;Acc:P14923] 0.0373336 0.147992 0.25226769 JUP
1075 TAX INTERACTION PROTEIN 1. [RefSeq;Acc:NM_014604] 0.281064 1.11415 0.252267648 no value
1076 "EXONUCLEASE 1 ISOFORM B; RAD2 NUCLEASE FAMILY MEMBER, HOMOLOG OF S. CEREVISIAE EXONUCLEASE 1. [RefSeq;Acc:NM_006027]" 0.03829 0.151786 0.252263055 EXO1
1077 PHD FINGER PROTEIN 9. [RefSeq;Acc:NM_018062] 0.0732296 0.290291 0.252262729 FANCL
1078 0.0349396 0.138505 0.252262373 UBE2W
1079 "SMALL OPTIC LOBES HOMOLOG; SMALL OPTIC LOBES, DROSOPHILA, HOMOLOG OF. [RefSeq;Acc:NM_005632]" 0.177598 0.704023 0.252261645 SOLH
1080 PRESENILINS ASSOCIATED RHOMBOID-LIKE PROTEIN. [RefSeq;Acc:NM_018622] 0.177185 0.702909 0.252073882 PARL
1081 0.0370737 0.147075 0.252073432 ZFAND1
1082 "GAMMA-BUTYROBETAINE,2-OXOGLUTARATE DIOXYGENASE (EC 1.14.11.1) (GAMMA-BUTYROBETAINE HYDROXYLASE) (GAMMA-BBH). [SWISSPROT;Acc:O75936]" 0.0513934 0.203883 0.252073003 BBOX1
1083 POTENTIAL PHOSPHOLIPID-TRANSPORTING ATPASE IH (EC 3.6.3.1) (ATPASE CLASS I TYPE 11A) (ATPASE IS). [SWISSPROT;Acc:P98196] 0.0225037 0.0892747 0.252072536 ATP11A
1084 PROTEIN C20ORF4 (PROTEIN CGI-23) (PRO0225). [SWISSPROT;Acc:Q9Y312] 0.145632 0.577812 0.252040456 C20orf4
1085 GDP-MANNOSE PYROPHOSPHORYLASE B ISOFORM 1; MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE; AMPHOTERIN INDUCED GENE 3. [RefSeq;Acc:NM_013334] 0.223627 0.887589 0.251948819 GMPPB
1086 GDP-MANNOSE PYROPHOSPHORYLASE A; MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE (GDP). [RefSeq;Acc:NM_013335] 0.0389051 0.154417 0.251948296 GMPPA
1087 0.189368 0.752124 0.251777632 RPAP3
1088 "ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 1 SUBUNIT (MU-ADAPTIN 1) (ADAPTOR PROTEIN COMPLEX AP-1 MU-1 SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN MU-1 SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN ASSEMBLY PROTEIN COMPLEX 1 MEDIUM CHAIN 1) (CLATHRIN COAT ASSEMBLY PROTEIN A" 0.168157 0.668251 0.251637484 AP1M1
1089 0.113583 0.451392 0.251628296 RSPH10B
1090 PHAFIN 2; PH AND FYVE DOMAIN-CONTAINING PROTEIN 2. [RefSeq;Acc:NM_024613] 0.2305 0.916205 0.251581251 PLEKHF2
1091 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] 0.0411277 0.163477 0.251580956 SRD5A1
1092 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] 0.0324086 0.12882 0.2515805 SRD5A2
1093 "CASEIN KINASE II, ALPHA' CHAIN (CK II) (EC 2.7.1.37). [SWISSPROT;Acc:P19784]" 0.23379 0.929536 0.251512583 CSNK2A2
1094 "CASEIN KINASE II, ALPHA CHAIN (CK II) (EC 2.7.1.37). [SWISSPROT;Acc:P19138]" CSNK2A1P
1095 "ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 2 SUBUNIT (MU-ADAPTIN 2) (ADAPTOR PROTEIN COMPLEX AP-1 MU-2 SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN MU-2 SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN ASSEMBLY PROTEIN COMPLEX 1 MEDIUM CHAIN 2) (AP-MU CHAIN FAMILY MEMBER MU1B)." 0.138969 0.552694 0.251439314 AP1M2
1096 PHOSPHOGLYCERATE MUTASE 2 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13) (PHOSPHOGLYCERATE MUTASE ISOZYME M) (PGAM-M) (BPG-DEPENDENT PGAM 2) (MUSCLE-SPECIFIC PHOSPHOGLYCERATE MUTASE). [SWISSPROT;Acc:P15259] 0.0270059 0.10746 0.251311186 PGAM2
1097 PUTATIVE PHOSPHOGLYCERATE MUTASE 3 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13). [SWISSPROT;Acc:Q8N0Y7] 0.030826 0.122661 0.251310522 PGAM4
1098 0.335885 1.33654 0.251309351 CCDC42
1099 PHOSPHOGLYCERATE MUTASE 1 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13) (PHOSPHOGLYCERATE MUTASE ISOZYME B) (PGAM-B) (BPG-DEPENDENT PGAM 1). [SWISSPROT;Acc:P18669] 0.0322794 0.128445 0.251309121 no value
1100 ATP-CITRATE SYNTHASE (EC 2.3.3.8) (ATP-CITRATE (PRO-S-)-LYASE) (CITRATE CLEAVAGE ENZYME). [SWISSPROT;Acc:P53396] 0.157326 0.626348 0.251179855 ACLY

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/