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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1277 to 1326 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
320 adp-ribosylation factor 3. [swissprot;acc:p16587] Divided 0 11627.8 10958.2 1.0611
epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] 1 241.892 265.96 1.0995
melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Subtracted 88.2482 110.265 22.0168
zinc finger protein 277. [swissprot;acc:q9nrm2] 0 6279.56 5569.42 710.14
321 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] Divided 11634.4 10989.9 1.05864
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 1 241.892 265.959 1.09949
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Subtracted 0 10280.5 9574.98 705.52
trophinin. [swissprot;acc:q12816] 1 88.2482 110.265 22.0168
322 deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Divided 86.7483 78.8995 1.09948
estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] 0 11634.4 10989.9 1.05864
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Subtracted 10287.1 9583.27 703.83
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 1 231.969 210.064 21.905
323 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 242.238 264.11 21.872
60s ribosomal protein l23a. [swissprot;acc:p29316] Divided 241.884 265.945 1.09947
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Subtracted 0 12320.2 13018.5 698.3
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] Divided 17387.1 16427.3 1.05843
324 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] Subtracted 1 242.238 264.11 21.872
40s ribosomal protein s23. [swissprot;acc:p39028] Divided 243.944 268.195 1.09941
baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392] Subtracted 0 7101.79 6406.18 695.61
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Divided 17387.1 16427.3 1.05843
325 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] 1 243.944 268.195 1.09941
60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Subtracted 241.828 263.62 21.792
mesoderm induction early response 1. [refseq;acc:nm_020948] 0 3609 4302.5 693.5
mstp028 protein. [refseq;acc:nm_031954] Divided 7965.66 7528.21 1.05811
326 40s ribosomal protein s16. [swissprot;acc:p17008] Subtracted 1 241.828 263.62 21.792
60s ribosomal protein l5. [swissprot;acc:p46777] Divided 241.899 265.924 1.09932
dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] 0 11948.4 11295.6 1.05779
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] Subtracted 12953.2 12273.2 680
327 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] Divided 9897.29 10466.5 1.05751
60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Subtracted 1 241.83 263.615 21.785
dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] 0 10768.5 11444 675.5
dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Divided 1 243.817 267.962 1.09903
328 adp-ribosylation factor 3. [swissprot;acc:p16587] Subtracted 0 11627.8 10958.2 669.6
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Divided 1 258.437 235.183 1.09888
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Subtracted 240.801 262.34 21.539
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Divided 0 10897 11520 1.05717
329 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Subtracted 10301.4 10957.5 656.1
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 1 191.644 170.192 21.452
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Divided 312 284 1.09859
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] 0 15977.3 15115.5 1.05701
330 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] 1 312 284 1.09859
crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Subtracted 224.657 203.235 21.422
dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] 0 11948.4 11295.6 652.8
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Divided 12320.2 13018.5 1.05668
331 40s ribosomal protein s3a. [swissprot;acc:p49241] 10405.1 10992.4 1.05644
adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] Subtracted 11634.4 10989.9 644.5
doc-1 related protein (doc-1r). [swissprot;acc:o75956] Divided 1 312 284 1.09859
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Subtracted 224.647 203.242 21.405
332 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] 224.633 203.251 21.382
estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] 0 11634.4 10989.9 644.5

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/