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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 14872 to 14921 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1859 sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077] Ranked Subtracted 220.896 218.577 2.319
1860 40s ribosomal protein s24 (s19). [swissprot;acc:p16632] Measured 5184.45 5554.97 370.52
dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941] Squared Divided 26167.2 28674.1 1.0958
fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] Ranked Subtracted 202.386 200.086 2.3
heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795] Divided 217.895 215.547 1.01089
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Measured 6076.66 6463.13 1.0636
lanc lantibiotic synthetase component c-like 2; testis-specific adriamycin sensitivity protein; lanc (bacterial lantibiotic synthetase component c)-like 2; g protein-coupled receptor 69b. [refseq;acc:nm_018697] Squared Subtracted 25625 27835.7 2210.7
mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093] Rooted 56.5094 58.3923 1.8829
unc-119 protein homolog (retinal protein 4) (hrg4). [swissprot;acc:q13432] Divided 62.7784 64.64 1.02965
1861 26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556]
beta-catenin (pro2286). [swissprot;acc:p35222] Squared 26746.2 29303.5 1.09561
cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] Ranked 210.856 213.147 1.01087
deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366] Rooted Subtracted 64.3493 66.2289 1.8796
fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] Ranked 202.386 200.086 2.3
keratin associated protein 1.5. [refseq;acc:nm_031957] Measured Divided 6076.66 6463.14 1.0636
lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [refseq;acc:nm_006055] Squared Subtracted 25625 27835.7 2210.7
splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] Measured 4331.35 4700.91 369.56
1862 26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460] 5826 6195.48 369.48
aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728] Rooted 63.6973 65.5763 1.879
cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Ranked Divided 210.856 213.147 1.01087
dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] Squared 14336.6 15706.2 1.09553
mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] Rooted 63.2302 65.1018 1.0296
mitochondrial ribosomal protein l18. [refseq;acc:nm_014161] Squared Subtracted 24134.9 26345.3 2210.4
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Ranked 202.393 200.094 2.299
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] Measured Divided 6076.66 6463.13 1.0636
1863 adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186] Subtracted 5826 6195.48 369.48
fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] Ranked 202.41 200.115 2.295
g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] Squared Divided 26779 29336.9 1.09552
glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] Rooted Subtracted 65.9292 67.8076 1.8784
keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690] Measured Divided 6076.66 6463.14 1.0636
nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] Ranked 210.856 213.147 1.01087
nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946] Rooted 63.2302 65.1018 1.0296
seven in absentia homolog 1. [refseq;acc:nm_003031] Squared Subtracted 24121.1 26329.1 2208
1864 adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [swissprot;acc:p55263] Rooted 65.9292 67.8076 1.8784
camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] Squared 24796.3 27002 2205.7
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] Ranked Divided 203.071 200.89 1.01086
heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] Squared 26778.4 29336.2 1.09552
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Measured 6076.66 6463.14 1.0636
lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12] Rooted 63.2302 65.1018 1.0296
putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5] Ranked Subtracted 215.081 217.373 2.292
ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5] Measured 5826 6195.48 369.48
1865 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] Ranked 210.856 213.147 2.291
eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] Divided 221.639 224.046 1.01086
heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597] Squared 26777.3 29334.8 1.09551
mitochondrial precursor proteins import receptor (translocase of outer membrane tom70). [swissprot;acc:o94826] Rooted 63.2302 65.1018 1.0296
presynaptic protein sap97 (synapse-associated protein 97) (discs, large homolog 1) (hdlg). [swissprot;acc:q12959] Squared Subtracted 26584 28784.7 2200.7
protein x 0001. [refseq;acc:nm_016302] Rooted 65.9292 67.8076 1.8784
rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763] Measured 5826 6195.48 369.48
star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2] Divided 6076.66 6463.12 1.0636
1866 channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700] Squared Subtracted 26586.2 28786.6 2200.4

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
- 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/