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 final expected
Results: HTML CSV LaTeX Showing element 151 to 200 of 3206 in total
Rank
description
measured
Hugo
final
expected
151 "KH DOMAIN-CONTAINING, RNA-BINDING, SIGNAL TRANSDUCTION-ASSOCIATED PROTEIN 2; SAM68-LIKE MAMMALIAN PROTEIN 1. [RefSeq;Acc:NM_152688]" 0.187708 KHDRBS2 0.351266433 0.534375
152 T-LAK CELL-ORIGINATED PROTEIN KINASE; SPERMATOGENESIS-RELATED PROTEIN KINASE; PDZ-BINDING KINASE; PBK; MAPKK-LIKE PROTEIN KINASE; SERINE/THREONINE PROTEIN KINASE. [RefSeq;Acc:NM_018492] 0.0544673 PBK 0.351265962 0.15506
153 CCDC95
154 0.145659 C11orf60 0.351265708 0.414669
155 HOMEOBOX PROTEIN HOX-D9 (HOX-4C) (HOX-5.2). [SWISSPROT;Acc:P28356] 1.29995 HOXD9 0.351139491 3.70209
156 0.205566 DTX4 0.351025245 0.585616
157 DJ820B18.1 (SIMILAR TO NUCLEAR CAP BINDING PROTEIN) (FRAGMENT). [SPTREMBL;Acc:Q8WWK2] 0.293028 NCBP2L 0.350956535 0.834941
158 NEURALIZED-LIKE. [RefSeq;Acc:NM_004210] 0.096416 NEURL 0.350761798 0.274876
159 FORMIN BINDING PROTEIN 3; FAS-LIGAND ASSOCIATED FACTOR 1; HUNTINGTIN-INTERACTING PROTEIN A; NY-REN-6 ANTIGEN. [RefSeq;Acc:NM_017892] 0.429285 no value 0.350413851 1.22508
160 HUNTINGTIN-INTERACTING PROTEIN HYPA/FBP11 (FRAGMENT). [SPTREMBL;Acc:O75404] 0.40616 0.350131894 1.16002
161 PREIMPLANTATION PROTEIN 3; LIKELY ORTHOLOG OF PREIMPLANTATION PROTEIN 3. [RefSeq;Acc:NM_015387] 0.297365 MOBKL3 0.345686432 0.860216
162 DNAJ HOMOLOG SUBFAMILY B MEMBER 11 PRECURSOR (ER-ASSOCIATED DNAJ PROTEIN 3) (ERJ3) (ER-ASSOCIATED HSP40 CO-CHAPERONE) (HDJ9) (PWP1- INTERACTING PROTEIN 4). [SWISSPROT;Acc:Q9UBS4] 0.0661546 DNAJB11 0.345685889 0.191372
163 NUCLEAR PROTEIN UKP68. [RefSeq;Acc:NM_024824] 0.200368 ZC3H14 0.344195075 0.582135
164 MUSASHI 2 ISOFORM A. [RefSeq;Acc:NM_138962] 0.0370125 MSI2 0.344193464 0.107534
165 MUSASHI 1. [RefSeq;Acc:NM_002442] 0.0416456 MSI1 0.344192735 0.120995
166 20 KDA NUCLEAR CAP BINDING PROTEIN (NCBP 20 KDA SUBUNIT) (CBP20) (NCBP INTERACTING PROTEIN 1) (NIP1). [SWISSPROT;Acc:P52298] 0.43784 NCBP2 0.341977006 1.28032
167 IMPORTIN ALPHA-4 SUBUNIT (KARYOPHERIN ALPHA-4 SUBUNIT) (QIP1 PROTEIN). [SWISSPROT;Acc:O00629] 0.487065 KPNA4 0.341790406 1.42504
168 "TARGET OF EGR1, MEMBER 1 (NUCLEAR); TARGET OF EGR1, MEMBER 1. [RefSeq;Acc:NM_025077]" 0.12614 TOE1 0.341751129 0.369099
169 IMPORTIN ALPHA-3 SUBUNIT (KARYOPHERIN ALPHA-3 SUBUNIT) (SRP1-GAMMA). [SWISSPROT;Acc:O00505] 0.446026 KPNA3 0.341711677 1.30527
170 0.0714655 EPC2 0.340221179 0.210056
171 YME1-LIKE 1 ISOFORM 3; ATP-DEPENDENT METALLOPROTEASE FTSH1 HOMOLOG. [RefSeq;Acc:NM_014263] 0.747794 YME1L1 0.340220294 2.19797
172 PEF PROTEIN WITH A LONG N-TERMINAL HYDROPHOBIC DOMAIN (PEFLIN). [RefSeq;Acc:NM_012392] 0.318787 PEF1 0.338675013 0.941277
173 HUNTINGTIN INTERACTING PROTEIN C. [RefSeq;Acc:NM_012272] 0.630724 PRPF40B 0.338287762 1.86446
174 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN 70 KDA (U1 SNRNP 70 KDA) (SNRNP70) (U1-70K). [SWISSPROT;Acc:P08621] 0.819252 SNRP70 0.337343424 2.42854
175 PROTEIN ARGININE N-METHYLTRANSFERASE 4 (EC 2.1.1.-). [SWISSPROT;Acc:Q9NR22] 0.0382473 PRMT8 0.337343224 0.113378
176 PROTEIN ARGININE N-METHYLTRANSFERASE 1 (EC 2.1.1.-) (INTERFERON RECEPTOR 1-BOUND PROTEIN 4). [SWISSPROT;Acc:Q99873] 0.0413596 PRMT1 0.33734299 0.122604
177 REV1-LIKE; REV1 PROTEIN; REV1 (YEAST HOMOLOG)- LIKE. [RefSeq;Acc:NM_016316] 0.120377 REV1 0.337342611 0.356839
178 FILAMIN A (ALPHA-FILAMIN) (FILAMIN 1) (ENDOTHELIAL ACTIN-BINDING PROTEIN) (ABP-280) (NONMUSCLE FILAMIN). [SWISSPROT;Acc:P21333] 0.0413389 no value 0.337341994 0.122543
179 "FILAMIN B, BETA (ACTIN BINDING PROTEIN 278); BETA FILAMIN; FILAMIN 1 (ACTIN-BINDING PROTEIN-280)-LIKE; FILAMIN B, BETA (ACTIN-BINDING PROTEIN-278); FILAMIN B, BETA. [RefSeq;Acc:NM_001457]" 0.0376993 FLNB 0.33734184 0.111754
180 TRINUCLEOTIDE REPEAT CONTAINING 15. [RefSeq;Acc:NM_015575] 0.0561104 no value 0.336776904 0.16661
181 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 2 (EIF-3 BETA) (EIF3 P36) (EIF3I) (TGF-BETA RECEPTOR INTERACTING PROTEIN 1) (TRIP-1). [SWISSPROT;Acc:Q13347] 0.336662 EIF3I 0.336776504 0.99966
182 CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-3 (ACTIVATING TRANSCRIPTION FACTOR 3). [SWISSPROT;Acc:P18847] 0.101196 ATF3 0.334897574 0.30217
183 LUC7-LIKE 2; CGI-74 PROTEIN; CGI-59 PROTEIN. [RefSeq;Acc:NM_016019] 0.723587 LUC7L2 0.331602729 2.18209
184 LUC7-LIKE; SARCOPLASMIC RETICULUM PROTEIN LUC7B1. [RefSeq;Acc:NM_018032] 0.809232 LUC7L 0.331515233 2.44101
185 SIMILAR TO LIM DOMAIN ONLY 7 (FRAGMENT). [SPTREMBL;Acc:Q8N6M2] 0.253477 LIMCH1 0.329682007 0.768853
186 0.185143 KCTD9 0.329681151 0.561582
187 SH2 DOMAIN CONTAINING 3C; NOVEL SH2-CONTAINING PROTEIN 3; SH2 DOMAIN-CONTAINING 3C; LIKELY ORTHOLOG OF MOUSE CAS/HEF1-ASSOCIATED SIGNAL TRANSDUCER. [RefSeq;Acc:NM_005489] 0.122271 SH2D3C 0.328897676 0.37176
188 BREAST CANCER ANTIESTROGEN RESISTANCE 3. [RefSeq;Acc:NM_003567] 0.157948 BCAR3 0.328882929 0.480256
189 JM1 PROTEIN. [RefSeq;Acc:NM_014008] 0.458256 CCDC22 0.328315351 1.39578
190 CRK-ASSOCIATED SUBSTRATE (P130CAS) (BREAST CANCER ANTI-ESTROGEN RESISTANCE 1 PROTEIN). [SWISSPROT;Acc:P56945] 0.17117 BCAR1 0.326398066 0.524421
191 "T-COMPLEX PROTEIN 1, DELTA SUBUNIT (TCP-1-DELTA) (CCT-DELTA) (STIMULATOR OF TAR RNA BINDING). [SWISSPROT;Acc:P50991]" 0.081012 CCT4 0.326383601 0.248211
192 ENHANCER OF FILAMENTATION 1 (HEF1) (CRK-ASSOCIATED SUBSTRATE-RELATED PROTEIN) (CAS-L) (CASL) (PP105) (NEURAL PRECURSOR CELL EXPRESSED DEVELOPMENTALLY DOWN-REGULATED 9). [SWISSPROT;Acc:Q14511] 0.133951 NEDD9 0.326365083 0.410433
193 B9 PROTEIN; LIKELY ORTHOLOG OF MOUSE ENDOTHELIAL PRECURSOR PROTEIN B9. [RefSeq;Acc:NM_015681] 0.771001 B9D1 0.325715432 2.3671
194 MAD PROTEIN (MAX DIMERIZER). [SWISSPROT;Acc:Q05195] 0.116127 MXD1 0.322600987 0.359971
195 MAX INTERACTING PROTEIN 1 (MXI1 PROTEIN). [SWISSPROT;Acc:P50539] 0.10032 MXI1 0.322537086 0.311034
196 MAX-INTERACTING TRANSCRIPTIONAL REPRESSOR MAD4 (MAX-ASSOCIATED PROTEIN 4) (MAX DIMERIZATION PROTEIN 4). [SWISSPROT;Acc:Q14582] 0.0956601 MXD4 0.322514641 0.296607
197 "POLYMERASE (DNA DIRECTED) IOTA; RAD30 (S. CEREVISIAE) HOMOLOG B; POLYMERASE (DNA-DIRECTED), IOTA. [RefSeq;Acc:NM_007195]" 0.048504 POLI 0.322510722 0.150395
198 PAXILLIN. [SWISSPROT;Acc:P49023] 0.183967 PXN 0.322509787 0.570423
199 MAX DIMERIZATION PROTEIN 3; LIKELY ORTHOLOG OF MOUSE MAX DIMERIZATION PROTEIN 3. [RefSeq;Acc:NM_031300] 0.0936195 RAB24 0.322503359 0.29029
200 POLYADENYLATE-BINDING PROTEIN 3 (POLY(A)-BINDING PROTEIN 3) (PABP 3) (TESTIS-SPECIFIC POLY(A)-BINDING PROTEIN). [SWISSPROT;Acc:Q9H361] 0.0404812 PABPC3 0.321961617 0.125733

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/