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 5014 to 5063 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1254 goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Measured 10725.6 9896.32 1.0838
ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283] Ranked 219.354 224.7 1.02437
serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1] Rooted 62.4299 65.2404 1.04502
1255 gtp binding protein 2. [refseq;acc:nm_019096]
mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] Squared 22337.6 25320.9 1.13356
ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86] Ranked 219.354 224.7 1.02437
serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [swissprot;acc:p33172] Measured 5438.66 5893.87 1.0837
1256 cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941] Rooted 62.4299 65.2404 1.04502
huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] Measured 10719 9891.08 1.0837
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] Ranked 219.354 224.699 1.02437
transportin-sr; importin 12. [refseq;acc:nm_012470] Squared 22037.5 24968.1 1.13298
1257 dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135] Rooted 62.4299 65.2404 1.04502
espin. [refseq;acc:nm_031475] Ranked 219.354 224.7 1.02437
exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] Squared 22008 24929.4 1.13274
immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318] Measured 5438.66 5893.87 1.0837
1258 apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] Squared 23019.8 26073.1 1.13264
cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635] Ranked 219.354 224.7 1.02437
glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] Measured 6251.32 6774.12 1.08363
sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691] Rooted 62.4299 65.2404 1.04502
1259 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Squared 13834.4 15664 1.13225
cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850] Rooted 62.4299 65.2404 1.04502
epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204] Measured 5685.38 6157.7 1.08308
pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832] Ranked 219.354 224.7 1.02437
1260 lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980]
rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] Squared 31586.9 35762.8 1.1322
rad54-like protein; rad54 homolog. [refseq;acc:nm_003579] Measured 5754.84 6232.83 1.08306
sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137] Rooted 62.4299 65.2404 1.04502
1261 d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917] Ranked 219.354 224.7 1.02437
epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929] Measured 5685.34 6157.53 1.08305
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Squared 15483.8 17529.5 1.13212
xap-5 protein (hxc-26 protein). [swissprot;acc:q14320] Rooted 62.4299 65.2404 1.04502
1262 histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] 76.053 79.4727 1.04496
keratin associated protein 9.2. [refseq;acc:nm_031961] Ranked 219.353 224.678 1.02428
serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1] Measured 5894.47 6383.73 1.083
zinc finger protein 277. [swissprot;acc:q9nrm2] Squared 15483.8 17529.5 1.13212
1263 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] 16151.6 18284.1 1.13203
gtp binding protein 2. [refseq;acc:nm_019096] Measured 5894.47 6383.73 1.083
histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Rooted 76.024 79.4409 1.04495
mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] Ranked 171.231 167.177 1.02425
1264 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Rooted 67.018 70.0209 1.04481
cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941] Measured 5894.47 6383.73 1.083
endothelial-derived gene 1. [refseq;acc:nm_025205] Squared 26062.8 29502.8 1.13199
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Ranked 171.231 167.177 1.02425
1265 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Squared 13562.4 15352.3 1.13198
dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135] Measured 5894.47 6383.73 1.083
inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] Rooted 57.8563 55.3779 1.04475
udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] Ranked 171.231 167.177 1.02425
1266 casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] Rooted 57.9924 60.5835 1.04468
polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780] Squared 22590.9 25571.8 1.13195
rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Ranked 171.231 167.177 1.02425

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/