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 Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
description Network Comparison Type Rank Gene Hugo Interaction Map Value Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 101 to 150 of 515 in total
Network Comparison Type  : Subtracted
Value Type  : Ranked
Filtered  : 1
red  : 0
green  : 0
network_comparison  : 0
description
Rank
Hugo
Interaction Map
dna ligase i (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p18858] 3103 LIG1 High confidence
dna ligase iv (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p49917] 2808 LIG4
dna methyltransferase 1-associated protein 1 (dnmt1-associated protein 1) (dnmap1). [swissprot;acc:q9npf5] 2796 DMAP1
dna mismatch repair protein msh2. [swissprot;acc:p43246] 3151 MSH2
dna mismatch repair protein msh6 (muts-alpha 160 kda subunit) (g/t mismatch binding protein) (gtbp) (gtmbp) (p160). [swissprot;acc:p52701] 3045 MSH6
dna replication licensing factor mcm8 (minichromosome maintenance 8). [swissprot;acc:q9uja3] 3011 MCM8
dna-repair protein complementing xp-a cells (xeroderma pigmentosum group a complementing protein). [swissprot;acc:p23025] 2971 XPA
dna-repair protein complementing xp-f cell (xeroderma pigmentosum group f complementing protein) (dna excision repair protein ercc-4). [swissprot;acc:q92889] 2801 ERCC4
double-stranded rna-binding zinc finger protein jaz. [refseq;acc:nm_012279] 3054 ZNF346
5047 Low confidence
doublesex and mab-3 related transcription factor 3; testis-specific protein; dmrt-like family a3. [refseq;acc:nm_021240] 3187 DMRT3 High confidence
dual specificity protein phosphatase 11 (ec 3.1.3.48) (rna/rnp complex-intereracting phosphatase) (phosphatase that interacts with rna/rnp complex 1). [swissprot;acc:o75319] 2926 DUSP11
dynein 2 light intermediate chain. [refseq;acc:nm_016008] 2962 DYNC2LI1
dynein intermediate chain 1, axonemal (axonemal dynein intermediate chain 1). [swissprot;acc:q9ui46] 3029 DNAI1
ecotropic virus integration 1 site protein. [swissprot;acc:q03112] 3170 EVI1
ell-associated factor 2; uncharacterized bone marrow protein bm040; testosterone regulated apoptosis inducer and tumor suppressor. [refseq;acc:nm_018456] 2921 EAF2
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] 3027 TSFM
endosome-associated fyve-domain protein. [refseq;acc:nm_014733] 3200 ZFYVE16
enhancer of zeste homolog 1 (enx-2). [swissprot;acc:q92800] 3090 EZH1
enhancer of zeste homolog 2 (enx-1). [swissprot;acc:q15910] 3098 EZH2
ergic-53 protein precursor (er-golgi intermediate compartment 53 kda protein) (lectin, mannose-binding 1) (gp58) (intracellular mannose specific lectin mr60). [swissprot;acc:p49257] 3177 LMAN1
erythroid differentiation-related factor 1. [refseq;acc:nm_015608] 3095 C10orf137
eukaryotic initiation factor 4a-i (eif-4a-i) (eif4a-i). [swissprot;acc:p04765] 2868 SNORA67
eukaryotic initiation factor 4a-ii (eif-4a-ii) (eif4a-ii). [swissprot;acc:q14240] 2888 EIF4A2
exocyst complex component exo70. [swissprot;acc:q9upt5] 2781 EXOC7
ezrin-binding partner pace-1 isoform 1. [refseq;acc:nm_020423] 3228 SCYL3
fatty aldehyde dehydrogenase (ec 1.2.1.3) (aldehyde dehydrogenase, microsomal) (aldh class 3). [swissprot;acc:p51648] 3181 ALDH3A2
ferrochelatase, mitochondrial precursor (ec 4.99.1.1) (protoheme ferro-lyase) (heme synthetase). [swissprot;acc:p22830] 3185 FECH
fibrillin 1 precursor. [swissprot;acc:p35555] 2844 FBN1
fibrillin 2 precursor. [swissprot;acc:p35556] 2955 FBN2
fibrillin 3. [refseq;acc:nm_032447] 2939 FBN3
flap endonuclease-1 (ec 3.-.-.-) (maturation factor 1) (mf1). [swissprot;acc:p39748] 2831 FEN1
fructose-bisphosphate aldolase a (ec 4.1.2.13) (muscle-type aldolase) (lung cancer antigen ny-lu-1). [swissprot;acc:p04075] 2907 ALDOA
fructose-bisphosphate aldolase b (ec 4.1.2.13) (liver-type aldolase). [swissprot;acc:p05062] 2973 ALDOB
fructose-bisphosphate aldolase c (ec 4.1.2.13) (brain-type aldolase). [swissprot;acc:p09972] 3087 ALDOC
fyve-finger-containing rab5 effector protein rabenosyn-5. [refseq;acc:nm_022340] 2998 ZFYVE20
g protein-coupled receptor 66. [refseq;acc:nm_006056] 2815 NMUR1
gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920] 5029 GGTLA4 Low confidence
gamma-glutamyltransferase. [sptrembl;acc:q14390] 5053 GGTL4
gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440] 5054 GGT1
gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268] 5020 no value
gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269] 5055 GGTLA1
gamma-interferon inducible lysosomal thiol reductase precursor (gamma-interferon-inducible protein ip-30). [swissprot;acc:p13284] 3101 no value High confidence
gdp-fucose protein o-fucosyltransferase 1 precursor (ec 2.4.1.221) (peptide o-fucosyltransferase) (o-fuct-1). [swissprot;acc:q9h488] 3125 POFUT1
geranylgeranyl transferase type ii beta subunit (ec 2.5.1.-) (rab geranylgeranyltransferase beta subunit) (rab geranyl- geranyltransferase beta subunit) (rab gg transferase beta) (rab ggtase beta). [swissprot;acc:p53611] 2963 RABGGTB
glioma pathogenesis-related protein (glipr) (rtvp-1 protein). [swissprot;acc:p48060] 2953 GLIPR1
glioma tumor suppressor candidate region gene 2 protein (p60). [swissprot;acc:q9nzm5] 3104 SNORD23
glioma-amplified sequence-41; numa binding protein 1. [refseq;acc:nm_006530] 3007 YEATS4
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] 3058 GNPDA1
glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335] 2861 GNPDA2

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 HGNC identifier if it exists
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/