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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2151 to 2200 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
269 tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Rooted 1 66.1064 74.1074 1.12103
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Measured 4590.18 5575.52 1.21466
270 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Squared 0 2569.37 3201.81 1.24615
crk-like protein. [swissprot;acc:p46109] Rooted 1 66.1064 74.1074 1.12103
ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Ranked 0 10735.1 9891.37 1.0853
fad synthetase. [refseq;acc:nm_025207] 1 241.373 267.352 1.10763
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Measured 23640.2 19479.8 1.21358
ribosomal protein l10-like protein. [refseq;acc:nm_080746] 0 1217.96 1367.88 1.12309
transcription factor iib. [refseq;acc:nm_013242] Squared 1 64739.9 50300.6 1.28706
zinc finger protein 277. [swissprot;acc:q9nrm2] Rooted 0 90.4079 98.9265 1.09422
271 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Ranked 1 241.373 267.352 1.10763
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Measured 2554.89 3093.78 1.21092
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Squared 0 92.5367 74.2791 1.2458
histone h4. [swissprot;acc:p02304] Measured 21773.1 24446.3 1.12278
microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650] Rooted 17.4356 19.0526 1.09274
myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Ranked 10735.1 9891.37 1.0853
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Rooted 1 66.1064 74.1073 1.12103
splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Squared 64739.9 50300.6 1.28706
272 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 0 4225.7 5255.44 1.24369
60s ribosomal protein l15. [swissprot;acc:p39030] Measured 846.216 753.793 1.12261
adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Squared 1 36563.7 46971.1 1.28464
chromodomain y-like protein 2. [refseq;acc:nm_152342] Rooted 0 33.0227 30.2263 1.09252
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Measured 1 3858.52 4669.27 1.21012
ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Ranked 241.373 267.352 1.10763
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Rooted 66.1064 74.1074 1.12103
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Ranked 0 7163.55 7759.61 1.08321
273 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Squared 4224.07 5253.37 1.24367
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] Ranked 1 241.373 267.352 1.10763
eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Measured 3199.4 3870.8 1.20985
filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] Squared 16120.1 20665.7 1.28198
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Rooted 66.1064 74.1074 1.12103
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Measured 0 1410.81 1582.65 1.1218
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Rooted 24.598 26.8697 1.09235
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] Ranked 12748.1 11770.9 1.08302
274 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Squared 4214.44 5226.4 1.24012
brain protein 16. [refseq;acc:nm_016458] Measured 2155.75 2418.14 1.12172
chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] 1 3119.98 2579.49 1.20953
disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Ranked 0 10432.4 11298.4 1.08301
grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Rooted 1 66.1063 74.1068 1.12102
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Ranked 241.373 267.352 1.10763
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Squared 16120.1 20665.7 1.28198
testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] Rooted 0 32.8979 30.1206 1.09221
275 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 1 66.1048 74.0977 1.12091
cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Ranked 241.373 267.352 1.10763
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 0 10783 11674.1 1.08264
pnas-18. [sptrembl;acc:q9bzu3] Squared 14643.9 11814.6 1.23947
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] 1 16120.1 20665.7 1.28198
regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Measured 3119.98 2579.49 1.20953
swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075] 0 717.401 804.725 1.12172
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Rooted 32.8937 30.117 1.0922

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/