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 Network Comparison Type Value Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 401 to 450 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
201 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Divided 6075.04 4810.22 1.26294
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Subtracted 12069.5 10603.5 1466
202 calsyntenin-1 precursor. [swissprot;acc:o94985]
enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Divided 6076.09 4812.01 1.26269
203 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 9352.11 11757.8 1.25723
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Subtracted 12069.5 10603.5 1466
204 protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] 12069.4 1465.9
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Divided 5655.52 4512.19 1.25339
205 small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Subtracted 12069.4 10603.5 1465.9
206 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Divided 4577.5 5720.25 1.24965
gk001 protein. [refseq;acc:nm_020198] Subtracted 12069.4 10603.5 1465.9
207 calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 12065.2 10600.3 1464.9
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Divided 5961.43 4771.21 1.24946
208 calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Subtracted 12064.7 10599.9 1464.8
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Divided 5082.18 4068.78 1.24907
209 ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Subtracted 9926.61 11383.2 1456.59
voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Divided 5082.18 4068.78 1.24907
210 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Subtracted 5810.82 4355.61 1455.21
voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Divided 5082.21 4068.82 1.24906
211 luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Subtracted 5811.49 4358.13 1453.36
voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Divided 5082.27 4068.91 1.24905
212 transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] 5553.79 4446.72 1.24896
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Subtracted 7865.15 6416.68 1448.47
213 carboxypeptidase b precursor. [refseq;acc:nm_020361] 6265.8 7711.38 1445.58
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Divided 5553.79 4446.72 1.24896
214 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Subtracted 6265.79 7711.36 1445.57
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Divided 5086.49 4074.83 1.24827
215 plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Subtracted 6265.76 7711.31 1445.55
transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Divided 12888.4 16074 1.24717
216 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] Subtracted 11511 10067.9 1443.1
leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Divided 12886.8 16071.6 1.24714
217 proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Subtracted 7859.6 6417.18 1442.42
ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Divided 12886.8 16071.6 1.24714
218 proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Subtracted 7859.6 6417.18 1442.42
transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Divided 12886 16070.4 1.24712
219 transforming protein n-ras. [swissprot;acc:p01111] 12885.6 16069.8 1.24711
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Subtracted 7859.6 6417.18 1442.42
220 crk-like protein. [swissprot;acc:p46109]
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] Divided 33356.5 41482.5 1.24361
221 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Subtracted 7859.6 6417.18 1442.42
222 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Divided 33356.5 41482.5 1.24361
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Subtracted 7859.6 6417.18 1442.42
223 cytohesin 4. [swissprot;acc:q9uia0] Divided 33356.5 41482.5 1.24361
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Subtracted 7859.59 6417.18 1442.41
224 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Divided 33356.5 41482.5 1.24361
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Subtracted 7859.59 6417.18 1442.41
225 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] 7859.51 6417.19 1442.32
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Divided 7279.6 9035 1.24114

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/