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

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/