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.


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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 [...,...].
Network Comparison Type Gene Value Type description Rank network_comparison green Filtered Interaction Map red
Results: HTML CSV LaTeX Showing element 1930 to 1979 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
description
Rank
network_comparison
green
red
orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [swissprot;acc:p43354] 2141 1.00689 206.343 207.765
orphan nuclear receptor tr2. [swissprot;acc:p13056] 1545 1.01702 216.083 219.76
osteoclast stimulating factor 1. [swissprot;acc:q92882] 759 1.04952 243.289 231.809
ovarian carcinoma immunoreactive antigen. [refseq;acc:nm_017830] 2136 1.00696 222.788 221.248
oxidation resistance 1. [refseq;acc:nm_181354] 2051 1.00834 216.981 218.79
oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133] 2422 1.00359 218.984 218.2
oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [swissprot;acc:p55055] 2416
p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671] 1308 1.02343 213.439 218.44
p10-binding protein. [refseq;acc:nm_024491] 1611 1.01577 217.877 221.313
p28 ing5. [refseq;acc:nm_032329] 1917 1.01015 218.039 215.848
p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162] 2542 1.002 217.633 218.068
p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [swissprot;acc:q92831] 2733 1.00028 202.172 202.229
p47 protein isoform a. [refseq;acc:nm_016143] 2201 1.00654 212.254 213.642
p53-related protein kinase (ec 2.7.1.-) (nori-2). [swissprot;acc:q96s44] 2752 1.00007 221.716 221.7
p66 alpha. [refseq;acc:nm_017660] 1560 1.01651 170.455 167.687
paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367] 1844 1.01109 212.417 214.773
pak1 interacting protein 1; pak1-interacting protein; pak/plc-interacting protein 1. [refseq;acc:nm_017906] 3072 1 0.00001 0.00001
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 213 1.127 186.95 210.693
palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] 807 1.04425 221.785 212.386
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] 199 1.13729 276.059 242.735
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 24 1.31818 44 58
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 25
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 26
pantothenate kinase 4 (ec 2.7.1.33) (pantothenic acid kinase 4) (hpank4). [swissprot;acc:q9nve7] 2883 1 0.00001 0.00001
parafibromin. [refseq;acc:nm_024529] 917 1.03772 230.991 239.704
paraspeckle protein 1. [refseq;acc:nm_018282] 2533 1.00214 190.824 190.417
parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] 830 1.0428 222.222 231.734
partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] 965 1.03426 204.964 211.987
pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] 1555 1.01656 192.996 196.192
paxillin. [swissprot;acc:p49023] 436 1.07909 205.286 221.522
pbk1 protein. [sptrembl;acc:o76021] 983 1.03382 235.353 243.312
pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] 833 1.0428 222.222 231.734
pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399] 914 1.03801 218.878 210.863
pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] 925 1.03714 207.942 215.665
pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] 2460 1.00308 235.088 235.812
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] 928 1.03651 218.017 225.976
peptide deformylase, mitochondrial precursor (ec 3.5.1.88) (pdf) (polypeptide deformylase). [swissprot;acc:q9hbh1] 2884 1 0.00001 0.00001
peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] 1753 1.01256 217.362 220.091
peptidyl prolyl isomerase h; cyclophilin h. [refseq;acc:nm_006347] 1939 1.00988 196.319 198.258
peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] 2400 1.00374 183.083 182.4
peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] 1078 1.03045 179.697 174.387
peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526] 2076 1.00803 223.483 221.703
peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] 695 1.05471 214.405 226.135
peregrin (bromodomain and phd finger-containing protein 1) (br140 protein). [swissprot;acc:p55201] 2820 1 0.00001 0.00001
pericentrin 1; frount; nucleoporin nup75. [refseq;acc:nm_024844] 3015
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] 673 1.05664 214.355 226.497
peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162] 2573 1.00161 213.005 213.347
peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [swissprot;acc:p30044] 1124 1.02748 213.256 207.553
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] 2688 1.00085 194.392 194.557
peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] 1851 1.01096 216.08 218.448

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/