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 Value Type Network Comparison Type description Interaction Map Filtered red green 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
Network Comparison Type
description
red
green
network_comparison
201 Divided t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 4810.22 6075.04 1.26294
Subtracted translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] 10603.5 12069.5 1466
202 Divided 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] 4812.01 6076.09 1.26269
Subtracted calsyntenin-1 precursor. [swissprot;acc:o94985] 10603.5 12069.5 1466
203 Divided autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 11757.8 9352.11 1.25723
Subtracted 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] 10603.5 12069.5 1466
204 Divided small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 4512.19 5655.52 1.25339
Subtracted protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] 10603.5 12069.4 1465.9
205 Divided small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] 4512.19 5655.52 1.25339
Subtracted thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] 10603.5 12069.4 1465.9
206 Divided atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 5720.25 4577.5 1.24965
Subtracted gk001 protein. [refseq;acc:nm_020198] 10603.5 12069.4 1465.9
207 Divided splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 4771.21 5961.43 1.24946
Subtracted calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 10600.3 12065.2 1464.9
208 Divided voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] 4068.78 5082.18 1.24907
Subtracted calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 10599.9 12064.7 1464.8
209 Divided voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] 4068.78 5082.18 1.24907
Subtracted 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] 11383.2 9926.61 1456.59
210 Divided voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] 4068.82 5082.21 1.24906
Subtracted luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 4355.61 5810.82 1455.21
211 Divided voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 4068.91 5082.27 1.24905
Subtracted luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 4358.13 5811.49 1453.36
212 Divided 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] 4446.72 5553.79 1.24896
Subtracted wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 6416.68 7865.15 1448.47
213 Divided nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 4446.72 5553.79 1.24896
Subtracted carboxypeptidase b precursor. [refseq;acc:nm_020361] 7711.38 6265.8 1445.58
214 Divided voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 4074.83 5086.49 1.24827
Subtracted mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 7711.36 6265.79 1445.57
215 Divided transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] 16074 12888.4 1.24717
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 6265.76 1445.55
216 Divided leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] 16071.6 12886.8 1.24714
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 11511 1443.1
217 Divided ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] 16071.6 12886.8 1.24714
Subtracted proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 6417.18 7859.6 1442.42
218 Divided transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] 16070.4 12886 1.24712
Subtracted proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 6417.18 7859.6 1442.42
219 Divided transforming protein n-ras. [swissprot;acc:p01111] 16069.8 12885.6 1.24711
Subtracted tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] 6417.18 7859.6 1442.42
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 33356.5 1.24361
Subtracted crk-like protein. [swissprot;acc:p46109] 6417.18 7859.6 1442.42
221 Divided cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 41482.5 33356.5 1.24361
Subtracted proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] 6417.18 7859.6 1442.42
222 Divided cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 41482.5 33356.5 1.24361
Subtracted proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 6417.18 7859.6 1442.42
223 Divided cytohesin 4. [swissprot;acc:q9uia0] 41482.5 33356.5 1.24361
Subtracted tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 6417.18 7859.59 1442.41
224 Divided cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 41482.5 33356.5 1.24361
Subtracted proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 6417.18 7859.59 1442.41
225 Divided myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 9035 7279.6 1.24114
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 7859.51 1442.32

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/