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 Network Comparison Type Value Type description green Rank network_comparison red Filtered Interaction Map
Results: HTML CSV LaTeX Showing element 2508 to 2557 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
description
green
Rank
network_comparison
red
serine/threonine protein phosphatase 2b catalytic subunit, alpha isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, alpha isoform) (cam-prp catalytic subunit). [swissprot;acc:q08209] 213.436 1305 1.02344 218.439
serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [swissprot;acc:p16299] 213.44 1307 1.02343 218.44
serine/threonine protein phosphatase 2b catalytic subunit, gamma isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, gamma isoform) (calcineurin, testis-specific catalytic subunit) (cam-prp catalytic subunit). [swissprot;acc:p48454] 213.441 1306 218.441
serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [swissprot;acc:p33172] 220.847 1705 1.01358 223.846
serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] 195.794 2317 1.00493 194.834
serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] 128.553 2018 1.00907 127.397
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] 123.727 1814 1.01167 122.3
serine/threonine-protein kinase chk1 (ec 2.7.1.-). [swissprot;acc:o14757] 0.00001 2908 1 0.00001
serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] 216.682 2701 1.00066 216.539
serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532] 0.00001 3137 1 0.00001
serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] 218.03 2346 1.00448 217.057
serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] 207.785 447 1.07827 224.049
serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [swissprot;acc:p51956] 218.03 2347 1.00448 217.057
serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] 235.98 494 1.0718 220.172
serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] 235.979 492 220.171
serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] 495
serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013] 210.42 1411 1.02095 206.102
serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [swissprot;acc:q9p286] 1416
serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] 216.64 2176 1.00669 218.089
serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896] 228.797 1364 1.02194 223.885
serine/threonine-protein kinase receptor r3 precursor (ec 2.7.1.37) (skr3) (activin receptor-like kinase 1) (alk-1) (tgf-b superfamily receptor type i) (tsr-i). [swissprot;acc:p37023] 0.00001 2952 1 0.00001
serologically defined colon cancer antigen 16. [refseq;acc:nm_006649] 213.479 2089 1.0078 215.144
serpin b11. [swissprot;acc:q96p15] 234.511 795 1.04578 224.244
serpin b12. [swissprot;acc:q96p63] 218.984 2413 1.00359 218.2
seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591] 213.14 2118 1.007 214.632
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] 2117
sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] 213.22 1290 1.02414 218.368
sestrin 2 (hi95). [swissprot;acc:p58004] 213.219 1279 1.02415
sestrin 3. [swissprot;acc:p58005] 1278
set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] 253.197 417 1.08417 233.539
set protein (hla-dr associated protein ii) (phapii) (phosphatase 2a inhibitor i2pp2a). [swissprot;acc:q01105] 0.00001 3039 1 0.00001
seven in absentia homolog 1. [refseq;acc:nm_003031] 225.005 2234 1.00625 223.608
seven in absentia homolog 2. [refseq;acc:nm_005067] 224.869 2256 1.00592 223.546
sex comb on midleg homolog 1. [refseq;acc:nm_012236] 0.00001 3217 1 0.00001
sex comb on midleg-like 2; sex comb on midleg like 2. [refseq;acc:nm_006089] 3120
sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137] 213.889 1684 1.01407 216.899
sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691] 1682
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] 231.059 1004 1.03318 238.725
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] 202.088 228 1.12036 226.411
sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503] 0.00001 2794 1 0.00001
sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3] 2867
sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822] 216.981 2050 1.00834 218.79
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] 2058
sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368] 2056
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] 203.553 1718 1.01325 206.251
sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] 203.818 1716 1.01327 206.522
sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] 204.111 1713 1.01329 206.823
shc transforming protein. [swissprot;acc:p29353] 222.788 2125 1.00696 221.248
short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] 229.549 646 1.05914 216.731
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 228.784 202 1.13553 201.478

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/