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

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/