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.


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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2075 to 2124 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1038 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] High confidence 186.741 181.041 1.03148
block of proliferation 1. [swissprot;acc:q14137] Low confidence 201.77 196.996 1.02423
1039 dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622] High confidence 207.719 214.236 1.03137
hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] Low confidence 203.911 199.088 1.02423
1040 brain protein 44. [swissprot;acc:o95563] 182.902 178.58 1.0242
t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643] High confidence 163.24 168.359 1.03136
1041 heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] 186.774 181.099 1.03134
protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] Low confidence 200.541 195.802 1.0242
1042 aspartate aminotransferase, cytoplasmic (ec 2.6.1.1) (transaminase a) (glutamate oxaloacetate transaminase-1). [swissprot;acc:p17174] 203.079 198.289 1.02416
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] High confidence 186.799 181.127 1.03132
1043 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] 187.834 182.137 1.03128
heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] Low confidence 210.83 205.858 1.02415
1044 14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] 201.723 196.966
t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] High confidence 173.475 178.889 1.03121
1045 aspartate aminotransferase, mitochondrial precursor (ec 2.6.1.1) (transaminase a) (glutamate oxaloacetate transaminase-2). [swissprot;acc:p00505] Low confidence 203.088 198.3 1.02415
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] High confidence 115.817 119.432 1.03121
1046 double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] 173.475 178.889
red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [swissprot;acc:p24666] Low confidence 201.208 196.467 1.02413
1047 splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] 205.265 200.428
steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] High confidence 187.022 181.391 1.03104
1048 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] 187.96 182.308 1.031
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Low confidence 202.477 197.709 1.02412
1049 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] High confidence 211.449 217.998 1.03097
ubiquitin-conjugating enzyme e2 m (ec 6.3.2.19) (ubiquitin-protein ligase m) (ubiquitin carrier protein m) (nedd8-conjugating enzyme ubc12). [swissprot;acc:o76069] Low confidence 198.569 193.893 1.02412
1050 estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] High confidence 211.449 217.998 1.03097
protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] Low confidence 194.002 189.435 1.02411
1051 17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] High confidence 211.449 217.998 1.03097
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Low confidence 200.439 205.267 1.02409
1052 retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725] High confidence 211.449 217.998 1.03097
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Low confidence 200.439 205.267 1.02409
1053 c-mpl binding protein. [refseq;acc:nm_052879] 204.184 199.387 1.02406
proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] High confidence 207.04 200.84 1.03087
1054 60s ribosomal protein l21. [swissprot;acc:p46778] 223.958 217.263 1.03082
runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] Low confidence 210.793 205.841 1.02406
1055 hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] High confidence 219.01 212.468 1.03079
nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Low confidence 199.656 194.966 1.02406
1056 phenylalanine-trna synthetase. [refseq;acc:nm_006567] 202.569 197.815 1.02403
vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606] High confidence 219.01 212.468 1.03079
1057 asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]
phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] Low confidence 202.569 197.815 1.02403
1058 ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] High confidence 228.105 221.293 1.03078
bet5 homolog (multiple myeloma protein 2) (mum-2). [swissprot;acc:q9y5r8] Low confidence 198.804 194.142 1.02401
1059 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] High confidence 228.105 221.293 1.03078
cationic amino acid transporter-4 (cat-4) (cat4). [swissprot;acc:o43246] Low confidence 200.552 195.852 1.024
1060 nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] High confidence 218.162 211.648 1.03078
synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] Low confidence 203.527 198.76 1.02398
1061 elks protein. [refseq;acc:nm_015064] High confidence 218.162 211.648 1.03078
germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982] Low confidence 204.104 199.324 1.02398
1062 dna-crosslink repair gene snm1. [refseq;acc:nm_014881] 203.048 198.295 1.02397
zinc finger protein 174 (aw-1). [swissprot;acc:q15697] High confidence 269.963 278.239 1.03066

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/