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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final Gene expected Rank measured description Hugo
Results: HTML CSV LaTeX Showing element 251 to 300 of 3206 in total
final
expected
Rank
measured
description
Hugo
0.147637112 1.48145 2956 0.218717 A-RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE (EC 2.7.1.-) (A-RAF-1) (PROTO-ONCOGENE PKS). [SWISSPROT;Acc:P10398] ARAF
0.147639202 1.48848 2955 0.219758 RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE (EC 2.7.1.-) (RAF-1) (C-RAF). [SWISSPROT;Acc:P04049] RAF1
0.147674774 0.914083 2954 0.134987 CYCLIN G1 (CYCLIN G). [SWISSPROT;Acc:P51959] CCNG1
0.147674925 0.497941 2953 0.0735334 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 56 KDA REGULATORY SUBUNIT, EPSILON ISOFORM (PP2A, B SUBUNIT, B' EPSILON ISOFORM) (PP2A, B SUBUNIT, B56 EPSILON ISOFORM) (PP2A, B SUBUNIT, PR61 EPSILON ISOFORM) (PP2A, B SUBUNIT, R5 EPSILON ISOFORM). [SWISSPR" PPP2R5E
0.147674982 0.387696 2952 0.057253 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 56 KDA REGULATORY SUBUNIT, ALPHA ISOFORM (PP2A, B SUBUNIT, B' ALPHA ISOFORM) (PP2A, B SUBUNIT, B56 ALPHA ISOFORM) (PP2A, B SUBUNIT, PR61 ALPHA ISOFORM) (PP2A, B SUBUNIT, R5 ALPHA ISOFORM). [SWISSPROT;Acc:Q15" PPP2R5A
0.147675752 1.01194 2951 0.149439 CYCLIN G2. [SWISSPROT;Acc:Q16589] CCNG2
0.147730689 1.90278 2950 0.281099 B-RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE (EC 2.7.1.-) (P94) (V-RAF MURINE SARCOMA VIRAL ONCOGENE HOMOLOG B1). [SWISSPROT;Acc:P15056] BRAF
0.151473179 2.42367 2949 0.367121 "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]" PFKP
0.15159729 2.07226 2948 0.314149 "6-PHOSPHOFRUCTOKINASE, MUSCLE TYPE (EC 2.7.1.11) (PHOSPHOFRUCTOKINASE 1) (PHOSPHOHEXOKINASE) (PHOSPHOFRUCTO-1-KINASE ISOZYME A) (PFK-A) (PHOSPHOFRUCTOKINASE-M). [SWISSPROT;Acc:P08237]" PFKM
0.151608079 2.04623 2947 0.310225 "6-PHOSPHOFRUCTOKINASE, LIVER TYPE (EC 2.7.1.11) (PHOSPHOFRUCTOKINASE 1) (PHOSPHOHEXOKINASE) (PHOSPHOFRUCTO-1-KINASE ISOZYME B) (PFK-B). [SWISSPROT;Acc:P17858]" PFKL
0.152240511 1.38339 2946 0.210608 PROTEASOME SUBUNIT ALPHA TYPE 5 (EC 3.4.25.1) (PROTEASOME ZETA CHAIN) (MACROPAIN ZETA CHAIN) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX ZETA CHAIN). [SWISSPROT;Acc:P28066] PSMA5
0.152530807 0.679961 2945 0.103715 SLC30A9
0.154162184 0.382047 2944 0.0588972 SPLICING FACTOR 4 ISOFORM B; RNA-BINDING PROTEIN. [RefSeq;Acc:NM_021164] SF4
0.155081311 0.528466 2942 0.0819552 NUCLEOTIDE-BINDING PROTEIN 1 (NBP 1). [SWISSPROT;Acc:P53384] NUBP1
2943 NUCLEOTIDE BINDING PROTEIN 2 (NBP 2). [SWISSPROT;Acc:Q9Y5Y2] NUBP2
0.155175336 1.00293 2941 0.15563 CHROMOBOX PROTEIN HOMOLOG 5 (HETEROCHROMATIN PROTEIN 1 HOMOLOG ALPHA) (HP1 ALPHA) (ANTIGEN P25). [SWISSPROT;Acc:P45973] CBX5
0.155324845 1.02341 2940 0.158961 CHROMOBOX PROTEIN HOMOLOG 3 (HETEROCHROMATIN PROTEIN 1 HOMOLOG GAMMA) (HP1 GAMMA) (MODIFIER 2 PROTEIN) (HECH). [SWISSPROT;Acc:Q13185] CBX3
0.156327849 1.18579 2939 0.185372 CHROMOBOX PROTEIN HOMOLOG 1 (HETEROCHROMATIN PROTEIN 1 HOMOLOG BETA) (HP1 BETA) (MODIFIER 1 PROTEIN) (M31) (HETEROCHROMATIN PROTEIN P25). [SWISSPROT;Acc:P23197] CBX1
0.157068631 0.682084 2938 0.107134 VPS37B
0.157129816 0.417367 2937 0.0655808 TUMOR SUSCEPTIBILITY GENE 101 PROTEIN. [SWISSPROT;Acc:Q99816] TSG101
0.157207261 0.529029 2936 0.0831672 VPS37C
0.158415086 0.117937 2933 0.018683 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] RGS20
2934 RAP1 GTPASE-ACTIVATING PROTEIN 1 (RAP1GAP). [SWISSPROT;Acc:P47736] RAP1GAP
2935 CHROMOSOME 3P21.1 GENE SEQUENCE. [RefSeq;Acc:NM_013286] RBM15B
0.158415218 0.0920202 2932 0.0145774 REGULATOR OF G-PROTEIN SIGNALING 19 (RGS19) (G-ALPHA INTERACTING PROTEIN) (GAIP PROTEIN). [SWISSPROT;Acc:P49795] RGS19
0.158415339 1.89012 2931 0.299424 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(O), ALPHA SUBUNIT 1. [SWISSPROT;Acc:P09471]" GNAO1
0.158415417 0.0932586 2930 0.0147736 REGULATOR OF G-PROTEIN SIGNALING 17 (RGS17). [SWISSPROT;Acc:Q9UGC6] RGS17
0.158415473 0.0939662 2929 0.0148857 PUTATIVE RNA-BINDING PROTEIN 15 (RNA BINDING MOTIF PROTEIN 15) (ONE-TWENTY TWO PROTEIN). [SWISSPROT;Acc:Q96T37] RBM15
0.158415565 0.543689 2928 0.0861288 MOSAIC PROTEIN LGN. [SWISSPROT;Acc:P81274] GPSM2
0.158415883 0.0959121 2927 0.015194 TRANSCRIPTION FACTOR LBX1. [SWISSPROT;Acc:P52954] LBX1
0.163937834 1.08227 2926 0.177425 "MALATE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.1.1.37). [SWISSPROT;Acc:P40926]" MDH2
0.167353852 0.704322 2925 0.117871 NUP93
0.167806839 1.00248 2924 0.168223 RAD50 HOMOLOG ISOFORM 1. [RefSeq;Acc:NM_005732] RAD50
0.167885273 2.16723 2923 0.363846 CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT 1 (CKS-1) (SID1334) (PNAS-16 / PNAS-143). [SWISSPROT;Acc:P33551] no value
0.168005712 1.02934 2922 0.172935 LAG1 LONGEVITY ASSURANCE HOMOLOG 2 ISOFORM 1; L3 PIGMENT; TUMOR METASTASIS-SUPPRESSOR. [RefSeq;Acc:NM_022075] LASS2
0.168379781 1.80704 2921 0.304269 PNAS-18. [SPTREMBL;Acc:Q9BZU3] no value
0.16882224 0.750535 2920 0.126707 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]
0.169656022 0.293943 2919 0.0498692 HIRA-INTERACTING PROTEIN 5 (CGI-33). [SWISSPROT;Acc:Q9UMS0] NFU1
0.171324654 1.30736 2918 0.223983 "PYRUVATE CARBOXYLASE, MITOCHONDRIAL PRECURSOR (EC 6.4.1.1) (PYRUVIC CARBOXYLASE) (PCB). [SWISSPROT;Acc:P11498]" PC
0.171620977 0.904936 2917 0.155306 UBIQUITIN-CONJUGATING ENZYME E2 G2 (EC 6.3.2.19) (UBIQUITIN-PROTEIN LIGASE G2) (UBIQUITIN CARRIER PROTEIN G2). [SWISSPROT;Acc:P56554] UBE2G2
0.171621238 0.239274 2916 0.0410645 38 KDA FK-506 BINDING PROTEIN HOMOLOG (FKBPR38) (FK506-BINDING PROTEIN 8). [SWISSPROT;Acc:Q14318] FKBP8
0.173454678 0.470177 2915 0.0815544 JM4 PROTEIN. [RefSeq;Acc:NM_007213] PRAF2
0.173519646 0.751425 2914 0.130387 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] UBE2D2
0.173890365 0.601977 2913 0.104678 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] ARL6IP5
0.174141535 1.54054 2912 0.268272 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] AP2M1
0.174141808 0.241467 2911 0.0420495 ANKS6
0.17414193 0.427267 2910 0.0744051 RNA POLYMERASE I TRANSCRIPTION FACTOR RRN3. [RefSeq;Acc:NM_018427] RRN3
0.174142027 0.187331 2908 0.0326222 SAP30L
2909 "ATP-BINDING CASSETTE, SUB-FAMILY C, MEMBER 10; MULTIDRUG RESISTANCE-ASSOCIATED PROTEIN 7. [RefSeq;Acc:NM_033450]" ABCC10
0.174142084 0.332958 2907 0.057982 TMEM55A

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/