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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description Rank Gene measured expected final Hugo
Results: HTML CSV LaTeX Showing element 1658 to 1707 of 3206 in total
description
Rank
measured
expected
final
Hugo
FUSE-BINDING PROTEIN-INTERACTING REPRESSOR ISOFORM B; SIAH BINDING PROTEIN 1; PYRIMIDINE TRACT BINDING SPLICING FACTOR; RO RIBONUCLEOPROTEIN-BINDING PROTEIN 1; POLY-U BINDING SPLICING FACTOR PUF60. [RefSeq;Acc:NM_014281] 1932 0.0838403 0.361827 0.231713775 PUF60
FUSED TOES HOMOLOG; LIKELY ORTHOLOG OF MOUSE FUSED TOES. [RefSeq;Acc:NM_022476] 494 0.277907 1.01314 0.274302663 AKTIP
FZR1 PROTEIN; FIZZY-RELATED PROTEIN; CDC20-LIKE 1B. [RefSeq;Acc:NM_016263] 3092 0.048624 0.498014 0.097635809 FZR1
G-RICH SEQUENCE FACTOR-1 (GRSF-1). [SWISSPROT;Acc:Q12849] 365 0.170665 0.610067 0.279747962 GRSF1
G1 TO S PHASE TRANSITION PROTEIN 1 HOMOLOG (GTP-BINDING PROTEIN GST1-HS). [SWISSPROT;Acc:P15170] 973 0.117727 0.460892 0.255432943 GSPT1
G2/MITOTIC-SPECIFIC CYCLIN B1. [SWISSPROT;Acc:P14635] 2896 0.163112 0.9315 0.175106817 CCNB1
G2/MITOTIC-SPECIFIC CYCLIN B2. [SWISSPROT;Acc:O95067] 2898 0.201803 1.15298 0.175027321 CCNB2
GA BINDING PROTEIN ALPHA CHAIN (GABP-ALPHA SUBUNIT) (TRANSCRIPTION FACTOR E4TF1-60) (NUCLEAR RESPIRATORY FACTOR-2 SUBUNIT ALPHA). [SWISSPROT;Acc:Q06546] 331 0.133623 0.468587 0.28516156 GABPA
GA BINDING PROTEIN BETA-2 CHAIN (GABP-BETA-2 SUBUNIT) (TRANSCRIPTION FACTOR E4TF1-47) (GAPBP-2) (NUCLEAR RESPIRATORY FACTOR-2 SUBUNIT GAMMA). [SWISSPROT;Acc:Q06545] 333 0.0373117 0.130845 0.28515954 no value
GABA(A) RECEPTOR-ASSOCIATED PROTEIN; GABA(A)-RECEPTOR-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_007278] 3036 0.125771 1.12068 0.112227398 GABARAP
GABA-A RECEPTOR-ASSOCIATED PROTEIN. [SPTREMBL;Acc:Q9BY60] 3001 0.0506272 0.392576 0.128961526 no value
GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE (EC 2.7.7.12) (GAL-1-P URIDYLYLTRANSFERASE) (UDP-GLUCOSE--HEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE). [SWISSPROT;Acc:P07902] 2677 0.0454701 0.217847 0.208724931
GALECTIN-4 (LACTOSE-BINDING LECTIN 4) (L-36 LACTOSE BINDING PROTEIN) (L36LBP) (ANTIGEN NY-CO-27). [SWISSPROT;Acc:P56470] 2466 0.384329 1.77366 0.216686964 LGALS4
GALECTIN-9 (HOM-HD-21) (ECALECTIN). [SWISSPROT;Acc:O00182] 2478 0.522708 2.41413 0.216520237 LGALS9
GAMMA ADDUCIN (ADDUCIN-LIKE PROTEIN 70). [SWISSPROT;Acc:Q9UEY8] 1456 0.183757 0.755771 0.243138464 ADD3
GAMMA ENOLASE (EC 4.2.1.11) (2-PHOSPHO-D-GLYCERATE HYDRO-LYASE) (NEURAL ENOLASE) (NSE) (ENOLASE 2). [SWISSPROT;Acc:P09104] 2216 0.0496823 0.22089 0.224918738 ENO2
GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-1 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P14867] 143 0.211371 0.601543 0.351381364 GABRA1
GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-2 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P47869] 144 0.211718 0.602532 0.351380508 GABRA2
GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-3 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P34903] 141 0.2125 0.604755 0.351381965 GABRA3
GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-4 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P48169] 140 0.217015 0.617604 0.351382115 GABRA4
GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-6 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:Q16445] 142 0.218317 0.62131 0.351381758 GABRA6
GAMMA-AMINOBUTYRIC-ACID RECEPTOR EPSILON SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P78334] 139 0.219446 0.624522 0.351382337 GABRE
GAMMA-AMINOBUTYRIC-ACID RECEPTOR GAMMA-1 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:Q8N1C3] 138 0.248966 0.708531 0.351383355 GABRG1
GAMMA-AMINOBUTYRIC-ACID RECEPTOR GAMMA-2 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P18507] 137 0.250789 0.713719 0.351383388 GABRG2
GAMMA-AMINOBUTYRIC-ACID RECEPTOR GAMMA-3 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:Q99928] 133 0.290469 0.826637 0.351386401 GABRG3
GAMMA-SARCOGLYCAN (GAMMA-SG) (35 KDA DYSTROPHIN-ASSOCIATED GLYCOPROTEIN) (35DAG). [SWISSPROT;Acc:Q13326] 1877 0.0566858 0.243524 0.232772951 SGCG
GAMMA-SNAP-ASSOCIATED FACTOR 1; RAB11-INTERACTING PROTEIN. [RefSeq;Acc:NM_015470] 765 0.0460867 0.174809 0.263640316 RAB11FIP5
GANGLIOSIDE-INDUCED DIFFERENTIATION-ASSOCIATED PROTEIN 1-LIKE 1. [RefSeq;Acc:NM_024034] 1745 0.0826697 0.349234 0.236717215 GDAP1L1
GANGLIOSIDE-INDUCED DIFFERENTIATION-ASSOCIATED PROTEIN 1. [RefSeq;Acc:NM_018972] 1748 0.0973611 0.411298 0.236716687 GDAP1
GASTRICSIN PRECURSOR (EC 3.4.23.3) (PEPSINOGEN C). [SWISSPROT;Acc:P20142] 2359 0.0442218 0.200737 0.220297205 PGC
GBP PROTEIN ISOFORM A. [RefSeq;Acc:NM_017870] 1148 0.0424223 0.169541 0.250218531 TMEM132A
GC-RICH SEQUENCE DNA-BINDING FACTOR HOMOLOG. [SWISSPROT;Acc:Q9Y5B6] 1558 0.037683 0.156176 0.241285473 C21orf66
GCN5-LIKE PROTEIN 1 (RT14 PROTEIN). [SWISSPROT;Acc:P78537] 1564 0.223546 0.927081 0.241128877 BLOC1S1
GDP-MANNOSE PYROPHOSPHORYLASE A; MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE (GDP). [RefSeq;Acc:NM_013335] 1086 0.0389051 0.154417 0.251948296 GMPPA
GDP-MANNOSE PYROPHOSPHORYLASE B ISOFORM 1; MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE; AMPHOTERIN INDUCED GENE 3. [RefSeq;Acc:NM_013334] 1085 0.223627 0.887589 0.251948819 GMPPB
GENERAL CONTROL OF AMINO ACID SYNTHESIS PROTEIN 5-LIKE 2 (EC 2.3.1.-) (HISTONE ACETYLTRANSFERASE GCN5) (HSGCN5). [SWISSPROT;Acc:Q92830] 2419 0.146069 0.669424 0.218201021 GCN5L2
GENERAL VESICULAR TRANSPORT FACTOR P115 (TRANSCYTOSIS ASSOCIATED PROTEIN) (TAP) (VESICLE DOCKING PROTEIN). [SWISSPROT;Acc:O60763] 404 1.73296 6.22802 0.278252157 USO1
GERANYLGERANYL PYROPHOSPHATE SYNTHETASE (GGPP SYNTHETASE) (GGPPSASE) (GERANYLGERANYL DIPHOSPHATE SYNTHASE) [INCLUDES: DIMETHYLALLYLTRANSFERASE (EC 2.5.1.1); GERANYLTRANSTRANSFERASE (EC 2.5.1.10); FARNESYLTRANSTRANSFERASE (EC 2.5.1.29)]. [SWISSPROT; 2439 0.265861 1.22405 0.217197827 GGPS1
GERANYLGERANYL TRANSFERASE TYPE I BETA SUBUNIT (EC 2.5.1.-) (TYPE I PROTEIN GERANYL-GERANYLTRANSFERASE BETA SUBUNIT) (GGTASE-I-BETA). [SWISSPROT;Acc:P53609] 926 0.0378747 0.146984 0.257679067 PGGT1B
GERM CELL SPECIFIC Y-BOX BINDING PROTEIN; CONTRIN. [RefSeq;Acc:NM_015982] 2191 0.0582372 0.257278 0.226359036 YBX2
GERM CELL-LESS. [RefSeq;Acc:NM_022471] 1060 0.398407 1.57699 0.25263762 no value
GK001 PROTEIN. [RefSeq;Acc:NM_020198] 2834 0.157265 0.814552 0.193069319 CCDC47
GLIA MATURATION FACTOR GAMMA (GMF-GAMMA). [SWISSPROT;Acc:O60234] 1517 0.0675774 0.278856 0.242337981 GMFG
GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 1 (EC 2.6.1.16) (HEXOSEPHOSPHATE AMINOTRANSFERASE 1) (D-FRUCTOSE-6- PHOSPHATE AMIDOTRANSFERASE 1) (GFAT 1) (GFAT1). [SWISSPROT;Acc:Q06210] 2231 0.61026 2.72155 0.224232515 no value
GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 2 (EC 2.6.1.16) (HEXOSEPHOSPHATE AMINOTRANSFERASE 2) (D-FRUCTOSE-6- PHOSPHATE AMIDOTRANSFERASE 2) (GFAT 2) (GFAT2). [SWISSPROT;Acc:O94808] 2240 0.687281 3.07116 0.223785475 GFPT2
GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE (EC 1.1.1.49) (G6PD). [SWISSPROT;Acc:P11413] 2426 0.146042 0.670248 0.217892482 G6PD
GLUCOSE-6-PHOSPHATE ISOMERASE (EC 5.3.1.9) (GPI) (PHOSPHOGLUCOSE ISOMERASE) (PGI) (PHOSPHOHEXOSE ISOMERASE) (PHI) (NEUROLEUKIN) (NLK) (SPERM ANTIGEN-36) (SA-36). [SWISSPROT;Acc:P06744] 2485 0.13384 0.618915 0.216249404 GPI
GLUTAMATE CARBOXYPEPTIDASE-LIKE PROTEIN 2 PRECURSOR. [SWISSPROT;Acc:Q96KN2] 2305 0.194519 0.875357 0.222216764 CNDP1
GLUTAMATE--CYSTEINE LIGASE CATALYTIC SUBUNIT (EC 6.3.2.2) (GAMMA- GLUTAMYLCYSTEINE SYNTHETASE) (GAMMA-ECS) (GCS HEAVY CHAIN). [SWISSPROT;Acc:P48506] 2743 0.027794 0.135904 0.204512008 GCLC
GLUTAMATE--CYSTEINE LIGASE REGULATORY SUBUNIT (EC 6.3.2.2) (GAMMA- GLUTAMYLCYSTEINE SYNTHETASE) (GAMMA-ECS) (GCS LIGHT CHAIN) (GLUTAMATE--CYSTEINE LIGASE MODIFIER SUBUNIT). [SWISSPROT;Acc:P48507] 2746 0.0555879 0.271808 0.204511641 GCLM

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/