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

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/