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 2901 to 2950 of 3206 in total
Rank
description
measured
expected
final
Hugo
2901 P66 ALPHA. [RefSeq;Acc:NM_017660] 0.0379885 0.217449 0.174700734 GATAD2A
2902 TYROSINE AMINOTRANSFERASE (EC 2.6.1.5) (L-TYROSINE:2-OXOGLUTARATE AMINOTRANSFERASE) (TAT). [SWISSPROT;Acc:P17735] 0.174557 0.999179 0.174700429 no value
2903 60S RIBOSOMAL PROTEIN L22 (EPSTEIN-BARR VIRUS SMALL RNA ASSOCIATED PROTEIN) (EBER ASSOCIATED PROTEIN) (EAP) (HEPARIN BINDING PROTEIN HBP15). [SWISSPROT;Acc:P35268] 0.173712 0.997527 0.174142655
2904 "SIN3 ASSOCIATED POLYPEPTIDE P30; SIN3-ASSOCIATED POLYPEPTIDE, 30KD. [RefSeq;Acc:NM_003864]" 0.0253172 0.145382 0.174142604 SAP30
2905 0.024304 0.139564 0.174142329 PLEKHG2
2906 "LYSOSOMAL ALPHA-MANNOSIDASE PRECURSOR (EC 3.2.1.24) (MANNOSIDASE, ALPHA B) (LYSOSOMAL ACID ALPHA-MANNOSIDASE) (LAMAN) (MANNOSIDASE ALPHA CLASS 2B MEMBER 1). [SWISSPROT;Acc:O00754]" 0.0662042 0.380173 0.174142298 MAN2B1
2907 0.057982 0.332958 0.174142084 TMEM55A
2908 0.0326222 0.187331 0.174142027 SAP30L
2909 "ATP-BINDING CASSETTE, SUB-FAMILY C, MEMBER 10; MULTIDRUG RESISTANCE-ASSOCIATED PROTEIN 7. [RefSeq;Acc:NM_033450]" ABCC10
2910 RNA POLYMERASE I TRANSCRIPTION FACTOR RRN3. [RefSeq;Acc:NM_018427] 0.0744051 0.427267 0.17414193 RRN3
2911 0.0420495 0.241467 0.174141808 ANKS6
2912 CLATHRIN COAT ASSEMBLY PROTEIN AP50 (CLATHRIN COAT ASSOCIATED PROTEIN AP50) (PLASMA MEMBRANE ADAPTOR AP-2 50 KDA PROTEIN) (HA2 50 KDA SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 MEDIUM CHAIN) (AP-2 MU 2 CHAIN). [SWISSPROT;Acc:P20172] 0.268272 1.54054 0.174141535 AP2M1
2913 CYTOSKELETON RELATED VITAMIN A RESPONSIVE PROTEIN; GLUTAMATE TRANSPORTER EEAC1-ASSOCIATED PROTEIN; DERMAL PAPILLA DERIVED PROTEIN 11; PUTATIVE MAPK ACTIVATING PROTEIN PM27. [RefSeq;Acc:NM_006407] 0.104678 0.601977 0.173890365 ARL6IP5
2914 UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2 (EC 6.3.2.19) (UBIQUITIN- PROTEIN LIGASE) (UBIQUITIN CARRIER PROTEIN) (E2(17)KB 2). [SWISSPROT;Acc:P51669] 0.130387 0.751425 0.173519646 UBE2D2
2915 JM4 PROTEIN. [RefSeq;Acc:NM_007213] 0.0815544 0.470177 0.173454678 PRAF2
2916 38 KDA FK-506 BINDING PROTEIN HOMOLOG (FKBPR38) (FK506-BINDING PROTEIN 8). [SWISSPROT;Acc:Q14318] 0.0410645 0.239274 0.171621238 FKBP8
2917 UBIQUITIN-CONJUGATING ENZYME E2 G2 (EC 6.3.2.19) (UBIQUITIN-PROTEIN LIGASE G2) (UBIQUITIN CARRIER PROTEIN G2). [SWISSPROT;Acc:P56554] 0.155306 0.904936 0.171620977 UBE2G2
2918 "PYRUVATE CARBOXYLASE, MITOCHONDRIAL PRECURSOR (EC 6.4.1.1) (PYRUVIC CARBOXYLASE) (PCB). [SWISSPROT;Acc:P11498]" 0.223983 1.30736 0.171324654 PC
2919 HIRA-INTERACTING PROTEIN 5 (CGI-33). [SWISSPROT;Acc:Q9UMS0] 0.0498692 0.293943 0.169656022 NFU1
2920 UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 3 (EC 6.3.2.19) (UBIQUITIN- PROTEIN LIGASE) (UBIQUITIN CARRIER PROTEIN) (E2(17)KB 3). [SWISSPROT;Acc:P47986] 0.126707 0.750535 0.16882224 no value
2921 PNAS-18. [SPTREMBL;Acc:Q9BZU3] 0.304269 1.80704 0.168379781
2922 LAG1 LONGEVITY ASSURANCE HOMOLOG 2 ISOFORM 1; L3 PIGMENT; TUMOR METASTASIS-SUPPRESSOR. [RefSeq;Acc:NM_022075] 0.172935 1.02934 0.168005712 LASS2
2923 CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT 1 (CKS-1) (SID1334) (PNAS-16 / PNAS-143). [SWISSPROT;Acc:P33551] 0.363846 2.16723 0.167885273 no value
2924 RAD50 HOMOLOG ISOFORM 1. [RefSeq;Acc:NM_005732] 0.168223 1.00248 0.167806839 RAD50
2925 0.117871 0.704322 0.167353852 NUP93
2926 "MALATE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.1.1.37). [SWISSPROT;Acc:P40926]" 0.177425 1.08227 0.163937834 MDH2
2927 TRANSCRIPTION FACTOR LBX1. [SWISSPROT;Acc:P52954] 0.015194 0.0959121 0.158415883 LBX1
2928 MOSAIC PROTEIN LGN. [SWISSPROT;Acc:P81274] 0.0861288 0.543689 0.158415565 GPSM2
2929 PUTATIVE RNA-BINDING PROTEIN 15 (RNA BINDING MOTIF PROTEIN 15) (ONE-TWENTY TWO PROTEIN). [SWISSPROT;Acc:Q96T37] 0.0148857 0.0939662 0.158415473 RBM15
2930 REGULATOR OF G-PROTEIN SIGNALING 17 (RGS17). [SWISSPROT;Acc:Q9UGC6] 0.0147736 0.0932586 0.158415417 RGS17
2931 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(O), ALPHA SUBUNIT 1. [SWISSPROT;Acc:P09471]" 0.299424 1.89012 0.158415339 GNAO1
2932 REGULATOR OF G-PROTEIN SIGNALING 19 (RGS19) (G-ALPHA INTERACTING PROTEIN) (GAIP PROTEIN). [SWISSPROT;Acc:P49795] 0.0145774 0.0920202 0.158415218 RGS19
2933 REGULATOR OF G-PROTEIN SIGNALING 20 (RGS20) (REGULATOR OF GZ- SELECTIVE PROTEIN SIGNALING 1) (GZ-SELECTIVE GTPASE-ACTIVATING PROTEIN) (G(Z)GAP). [SWISSPROT;Acc:O76081] 0.018683 0.117937 0.158415086 RGS20
2934 RAP1 GTPASE-ACTIVATING PROTEIN 1 (RAP1GAP). [SWISSPROT;Acc:P47736] RAP1GAP
2935 CHROMOSOME 3P21.1 GENE SEQUENCE. [RefSeq;Acc:NM_013286] RBM15B
2936 0.0831672 0.529029 0.157207261 VPS37C
2937 TUMOR SUSCEPTIBILITY GENE 101 PROTEIN. [SWISSPROT;Acc:Q99816] 0.0655808 0.417367 0.157129816 TSG101
2938 0.107134 0.682084 0.157068631 VPS37B
2939 CHROMOBOX PROTEIN HOMOLOG 1 (HETEROCHROMATIN PROTEIN 1 HOMOLOG BETA) (HP1 BETA) (MODIFIER 1 PROTEIN) (M31) (HETEROCHROMATIN PROTEIN P25). [SWISSPROT;Acc:P23197] 0.185372 1.18579 0.156327849 CBX1
2940 CHROMOBOX PROTEIN HOMOLOG 3 (HETEROCHROMATIN PROTEIN 1 HOMOLOG GAMMA) (HP1 GAMMA) (MODIFIER 2 PROTEIN) (HECH). [SWISSPROT;Acc:Q13185] 0.158961 1.02341 0.155324845 CBX3
2941 CHROMOBOX PROTEIN HOMOLOG 5 (HETEROCHROMATIN PROTEIN 1 HOMOLOG ALPHA) (HP1 ALPHA) (ANTIGEN P25). [SWISSPROT;Acc:P45973] 0.15563 1.00293 0.155175336 CBX5
2942 NUCLEOTIDE-BINDING PROTEIN 1 (NBP 1). [SWISSPROT;Acc:P53384] 0.0819552 0.528466 0.155081311 NUBP1
2943 NUCLEOTIDE BINDING PROTEIN 2 (NBP 2). [SWISSPROT;Acc:Q9Y5Y2] NUBP2
2944 SPLICING FACTOR 4 ISOFORM B; RNA-BINDING PROTEIN. [RefSeq;Acc:NM_021164] 0.0588972 0.382047 0.154162184 SF4
2945 0.103715 0.679961 0.152530807 SLC30A9
2946 PROTEASOME SUBUNIT ALPHA TYPE 5 (EC 3.4.25.1) (PROTEASOME ZETA CHAIN) (MACROPAIN ZETA CHAIN) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX ZETA CHAIN). [SWISSPROT;Acc:P28066] 0.210608 1.38339 0.152240511 PSMA5
2947 "6-PHOSPHOFRUCTOKINASE, LIVER TYPE (EC 2.7.1.11) (PHOSPHOFRUCTOKINASE 1) (PHOSPHOHEXOKINASE) (PHOSPHOFRUCTO-1-KINASE ISOZYME B) (PFK-B). [SWISSPROT;Acc:P17858]" 0.310225 2.04623 0.151608079 PFKL
2948 "6-PHOSPHOFRUCTOKINASE, MUSCLE TYPE (EC 2.7.1.11) (PHOSPHOFRUCTOKINASE 1) (PHOSPHOHEXOKINASE) (PHOSPHOFRUCTO-1-KINASE ISOZYME A) (PFK-A) (PHOSPHOFRUCTOKINASE-M). [SWISSPROT;Acc:P08237]" 0.314149 2.07226 0.15159729 PFKM
2949 "6-PHOSPHOFRUCTOKINASE, TYPE C (EC 2.7.1.11) (PHOSPHOFRUCTOKINASE 1) (PHOSPHOHEXOKINASE) (PHOSPHOFRUCTO-1-KINASE ISOZYME C) (PFK-C) (6-PHOSPHOFRUCTOKINASE, PLATELET TYPE). [SWISSPROT;Acc:Q01813]" 0.367121 2.42367 0.151473179 PFKP
2950 B-RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE (EC 2.7.1.-) (P94) (V-RAF MURINE SARCOMA VIRAL ONCOGENE HOMOLOG B1). [SWISSPROT;Acc:P15056] 0.281099 1.90278 0.147730689 BRAF

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/