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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Gene Rank Network Comparison Type Value Type description Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 425 to 474 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
description
red
network_comparison
green
213 Divided nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 4446.72 1.24896 5553.79
Subtracted carboxypeptidase b precursor. [refseq;acc:nm_020361] 7711.38 1445.58 6265.8
214 Divided voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 4074.83 1.24827 5086.49
Subtracted mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 7711.36 1445.57 6265.79
215 Divided transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] 16074 1.24717 12888.4
Subtracted plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] 7711.31 1445.55 6265.76
216 Divided leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] 16071.6 1.24714 12886.8
Subtracted enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] 10067.9 1443.1 11511
217 Divided ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] 16071.6 1.24714 12886.8
Subtracted proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 6417.18 1442.42 7859.6
218 Divided transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] 16070.4 1.24712 12886
Subtracted proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 6417.18 1442.42 7859.6
219 Divided transforming protein n-ras. [swissprot;acc:p01111] 16069.8 1.24711 12885.6
Subtracted tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] 6417.18 1442.42 7859.6
220 Divided mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] 41482.5 1.24361 33356.5
Subtracted crk-like protein. [swissprot;acc:p46109] 6417.18 1442.42 7859.6
221 Divided cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 41482.5 1.24361 33356.5
Subtracted proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] 6417.18 1442.42 7859.6
222 Divided cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 41482.5 1.24361 33356.5
Subtracted proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 6417.18 1442.42 7859.6
223 Divided cytohesin 4. [swissprot;acc:q9uia0] 41482.5 1.24361 33356.5
Subtracted tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 6417.18 1442.41 7859.59
224 Divided cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 41482.5 1.24361 33356.5
Subtracted proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 6417.18 1442.41 7859.59
225 Divided myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 9035 1.24114 7279.6
Subtracted 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] 6417.19 1442.32 7859.51
226 Divided myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 9035 1.24114 7279.6
Subtracted ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 6417.31 1440.81 7858.12
227 Divided myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] 9035 1.24114 7279.6
Subtracted homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 6417.33 1440.6 7857.93
228 Divided myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] 9035 1.24114 7279.6
Subtracted neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 6417.81 1434.71 7852.52
229 Divided myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] 9035 1.24114 7279.6
Subtracted small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] 10434.4 1411.8 11846.2
230 Divided myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 9035 1.24114 7279.6
Subtracted 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] 9649.61 1403.89 11053.5
231 Divided myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] 9035 1.24114 7279.6
Subtracted sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] 9649.61 1403.89 11053.5
232 Divided dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] 9035 1.24114 7279.6
Subtracted 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] 9649.61 1403.89 11053.5
233 Divided myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 9035 1.24114 7279.6
Subtracted 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] 9649.61 1403.89 11053.5
234 Divided ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] 5181.2 1.23728 6410.58
Subtracted map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] 9649.61 1403.89 11053.5
235 Divided ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 5181.2 1.23728 6410.58
Subtracted neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] 9649.61 1403.89 11053.5
236 Divided spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 4723.53 1.23392 5828.46
Subtracted nitrogen fixation cluster-like. [refseq;acc:nm_014301] 9649.61 1403.89 11053.5
237 Divided u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 4567.04 1.23301 5631.2
Subtracted star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] 9649.61 1403.89 11053.5

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/