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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Value Type Gene description Rank Interaction Map Network Comparison Type red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1062 to 1111 of 3228 in total
Value Type  : Ranked
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1
description
Rank
red
green
network_comparison
ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] 726 244.495 232.419 1.05196
fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] 731 208.874 219.708 1.05187
fuse binding protein 3 (fragment). [sptrembl;acc:q92946] 2668 217.176 216.944 1.00107
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] 1864 203.071 200.89 1.01086
fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476] 2124 221.248 222.788 1.00696
fyve-finger-containing rab5 effector protein rabenosyn-5. [refseq;acc:nm_022340] 2998 0.00001 0.00001 1
fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] 848 147.211 153.371 1.04184
g protein-coupled receptor 66. [refseq;acc:nm_006056] 2815 0.00001 0.00001 1
g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] 1855 217.891 215.542 1.0109
g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] 1631 218.789 215.533 1.01511
g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] 1582 168.098 170.844 1.01634
g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] 1580 168.018 170.769 1.01637
ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] 883 227.596 219.017 1.03917
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] 884
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 48 65.4586 83.0461 1.26868
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 168 82.5916 98.0548 1.18722
galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] 1337 215.162 210.412 1.02257
galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] 2158 206.401 207.796 1.00676
galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] 2122 206.473 207.911 1.00696
gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] 1934 224.264 222.055 1.00995
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] 2360 207.186 208.046 1.00415
gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] 628 214.256 202.14 1.05994
gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] 621
gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] 629
gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] 625
gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] 622
gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 626
gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] 620
gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] 623
gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] 618 202.139
gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936] 1842 212.455 210.113 1.01115
gamma-interferon inducible lysosomal thiol reductase precursor (gamma-interferon-inducible protein ip-30). [swissprot;acc:p13284] 3101 0.00001 0.00001 1
gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] 1181 218.186 212.672 1.02593
gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470] 1817 220.462 217.926 1.01164
gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] 166 209.299 249.187 1.19058
ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] 1139 218.484 212.675 1.02731
ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] 1141
gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [swissprot;acc:p20142] 2470 235.812 235.088 1.00308
gbp protein isoform a. [refseq;acc:nm_017870] 47 325.586 256.492 1.26938
gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] 2539 217.144 216.699 1.00205
gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] 979 202.027 195.386 1.03399
gdp-fucose protein o-fucosyltransferase 1 precursor (ec 2.4.1.221) (peptide o-fucosyltransferase) (o-fuct-1). [swissprot;acc:q9h488] 3125 0.00001 0.00001 1
gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] 1894 222.842 225.17 1.01045
gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334] 1893
general control of amino acid synthesis protein 5-like 2 (ec 2.3.1.-) (histone acetyltransferase gcn5) (hsgcn5). [swissprot;acc:q92830] 2732 202.233 202.175 1.00029
general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763] 1923 220.659 218.452 1.0101
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;acc:o95749] 2536 236.51 236.008 1.00213
geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [swissprot;acc:p53609] 1438 225.039 229.573 1.02015
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 0.00001 0.00001 1
germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982] 2685 208.438 208.635 1.00095

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/