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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Gene Rank Network Comparison Type description Value Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
description
red
green
network_comparison
226 Divided cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 239.991 269.238 1.12187
Subtracted protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] 242.153 266.673 24.52
227 Divided thrombospondin 3 precursor. [swissprot;acc:p49746] 239.99 269.234 1.12186
Subtracted methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] 244.126 268.604 24.478
228 Divided 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] 226.411 202.088 1.12036
Subtracted methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] 244.126 268.604 24.478
229 Divided breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 226.401 202.094 1.12028
Subtracted 60s ribosomal protein l3-like. [swissprot;acc:q92901] 242.195 266.663 24.468
230 Divided cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 239.35 267.915 1.11934
Subtracted protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] 242.694 267.017 24.323
231 Divided likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 239.336 267.881 1.11927
Subtracted 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] 226.411 202.088 24.323
232 Divided smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] 239.336 267.879 1.11926
Subtracted breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 226.401 202.094 24.307
233 Divided lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] 239.32 267.842 1.11918
Subtracted 60s ribosomal protein l7. [swissprot;acc:p18124] 235.727 259.984 24.257
234 Divided chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 287.41 256.835 1.11905
Subtracted 40s ribosomal protein s23. [swissprot;acc:p39028] 243.944 268.195 24.251
235 Divided phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] 227.357 254.15 1.11785
Subtracted 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] 243.944 268.195 24.251
236 Divided pp3111 protein. [refseq;acc:nm_022156] 227.357 254.15 1.11785
Subtracted histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 252.644 228.42 24.224
237 Divided syntaxin 18. [swissprot;acc:q9p2w9] 227.357 254.15 1.11785
Subtracted mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] 242.011 266.18 24.169
238 Divided rd protein. [swissprot;acc:p18615] 227.357 254.15 1.11785
Subtracted metastasis-associated protein mta1. [swissprot;acc:q13330] 252.512 228.356 24.156
239 Divided glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 227.357 254.15 1.11785
Subtracted dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] 243.817 267.962 24.145
240 Divided androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] 227.357 254.15 1.11785
Subtracted chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] 252.39 228.297 24.093
241 Divided atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] 227.357 254.15 1.11785
Subtracted epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] 241.892 265.96 24.068
242 Divided j domain containing protein 1. [swissprot;acc:q9ukb3] 227.357 254.15 1.11785
Subtracted c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 241.892 265.959 24.067
243 Divided sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] 227.357 254.15 1.11785
Subtracted 60s ribosomal protein l23a. [swissprot;acc:p29316] 241.884 265.945 24.061
244 Divided ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 227.357 254.15 1.11785
Subtracted 60s ribosomal protein l5. [swissprot;acc:p46777] 241.899 265.924 24.025
245 Divided small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 226.109 202.333 1.11751
Subtracted 60s ribosomal protein l19. [swissprot;acc:p14118] 240.73 264.729 23.999
246 Divided eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 237.312 212.363 1.11748
Subtracted 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 243.583 267.528 23.945
247 Divided rna-binding protein. [refseq;acc:nm_019027] 237.302 212.41 1.11719
Subtracted 60s ribosomal protein l12. [swissprot;acc:p30050] 243.583 267.527 23.944
248 Divided apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 237.302 212.41 1.11719
Subtracted dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 243.583 267.527 23.944
249 Divided ns1-associated protein 1. [refseq;acc:nm_006372] 237.302 212.41 1.11719
Subtracted small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 226.109 202.333 23.776
250 Divided heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 237.302 212.41 1.11719
Subtracted pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 210.693 186.95 23.743

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/