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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description Rank Gene Value Type Network Comparison Type Filtered Interaction Map green red network_comparison
Results: HTML CSV LaTeX Showing element 1051 to 1100 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
description
Rank
Interaction Map
green
red
network_comparison
bone morphogenetic protein 6 precursor (bmp-6). [swissprot;acc:p22004] 2896 High confidence 0.00001 0.00001 1
2923 Low confidence 200.077 203.481 1.01701
bone morphogenetic protein 7 precursor (bmp-7) (osteogenic protein 1) (op-1). [swissprot;acc:p18075] 2943 200.059 203.455 1.01697
3128 High confidence 0.00001 0.00001 1
bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] 2773
2910 Low confidence 200.087 203.494 1.01703
brachyury protein (t protein). [swissprot;acc:o15178] 56 202.592 224.922 1.11022
2040 High confidence 208.803 210.586 1.00854
brain link protein-1 precursor. [swissprot;acc:q9gzv7] 2642 Low confidence 200.174 203.73 1.01776
brain protein 16. [refseq;acc:nm_016458] 1847 High confidence 219.195 216.811 1.011
2180 Low confidence 184.788 188.304 1.01903
brain protein 44-like protein (hspc040) (cgi-129) (pnas-115). [swissprot;acc:q9y5u8] 1080 191.803 196.378 1.02385
brain protein 44. [swissprot;acc:o95563] 742 High confidence 120.078 126.215 1.05111
1040 Low confidence 178.58 182.902 1.0242
branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] 1867 196.027 199.922 1.01987
2672 High confidence 210.741 210.957 1.00102
branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] 1877 Low confidence 195.99 199.88 1.01985
2687 High confidence 210.755 210.939 1.00087
brca1 associated protein. [refseq;acc:nm_006768] 3161 0.00001 0.00001 1
4538 Low confidence 176.223 177.657 1.00814
brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] 1752 High confidence 218.991 216.271 1.01258
3479 Low confidence 196.226 199.172 1.01501
brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] 294 High confidence 265.717 240.782 1.10356
1490 Low confidence 198.329 202.583 1.02145
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 229 High confidence 202.094 226.401 1.12028
603 Low confidence 195.587 201.427 1.02986
breast cancer antigen ny-br-1. [refseq;acc:nm_052997] 262 207.332 216.842 1.04587
breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] 939 High confidence 224.27 216.501 1.03588
3636 Low confidence 198.576 201.391 1.01418
breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 691 High confidence 206.195 217.602 1.05532
1733 Low confidence 198.294 202.346 1.02043
brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6] 647 197.621 203.293 1.0287
2713 High confidence 220.395 220.521 1.00057
brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] 649 Low confidence 197.617 203.283 1.02867
2711 High confidence 220.395 220.521 1.00057
brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 597 Low confidence 198.854 204.856 1.03018
945 High confidence 205.085 212.44 1.03586
bromodomain adjacent to zinc finger domain protein 1a (atp-utilizing chromatin assembly and remodeling factor 1) (hacf1) (atp-dependent chromatin remodelling protein) (williams syndrome transcription factor-related chromatin remodeling factor 180) (wcrf180) (hwalp1) (chrac subunit acf1) (hspc317). [swissprot;acc:q9nrl2] 183 Low confidence 206.947 196.372 1.05385
bromodomain and phd finger-containing protein 3 (fragment). [swissprot;acc:q9uld4] 3149 High confidence 0.00001 0.00001 1
3354 Low confidence 201.079 204.204 1.01554
bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263] 1002 200.227 205.137 1.02452
2747 High confidence 201.514 201.477 1.00018
bromodomain containing 8; thyroid hormone receptor coactivating protein; skeletal muscle abundant protein. [refseq;acc:nm_006696] 573 Low confidence 200.275 206.46 1.03088
bromodomain-containing protein 1 (br140-like protein). [swissprot;acc:o95696] 3139 High confidence 0.00001 0.00001 1
3352 Low confidence 201.079 204.204 1.01554
bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] 2241 High confidence 224.338 222.96 1.00618
3324 Low confidence 194.204 197.238 1.01562
bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] 2237 High confidence 224.343 222.965 1.00618
3350 Low confidence 194.055 197.071 1.01554
bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885] 2238 High confidence 224.337 222.959 1.00618

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/