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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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 [...,...].
description Rank Gene Value Type Network Comparison Type Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
description
Rank
Interaction Map
red
green
network_comparison
heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] 482 High confidence 237.109 254.667 1.07405
1043 Low confidence 210.83 205.858 1.02415
hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6] 2021 High confidence 208.601 210.464 1.00893
2432 Low confidence 198.399 194.819 1.01838
hexokinase d (ec 2.7.1.1) (hexokinase type iv) (hk iv) (hk4) (glucokinase). [swissprot;acc:p35557] 3465 200.291 197.312 1.0151
hexokinase type iii (ec 2.7.1.1) (hk iii). [swissprot;acc:p52790] 3462 200.296 197.315 1.01511
hexokinase, type i (ec 2.7.1.1) (hk i) (brain form hexokinase). [swissprot;acc:p19367] 3458 200.307 197.322 1.01513
hexokinase, type ii (ec 2.7.1.1) (hk ii) (muscle form hexokinase). [swissprot;acc:p52789] 3453 200.319 197.33 1.01515
high mobility group protein 1 (hmg-1). [swissprot;acc:p09429] 2834 204.765 201.302 1.0172
2989 High confidence 0.00001 0.00001 1
high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6] 2842 Low confidence 204.741 201.28 1.01719
3144 High confidence 0.00001 0.00001 1
high mobility group protein 2 (hmg-2). [swissprot;acc:p26583] 2831 Low confidence 204.584 201.125 1.0172
2856 High confidence 0.00001 0.00001 1
high mobility group protein 4 (hmg-4) (high mobility group protein 2a) (hmg-2a). [swissprot;acc:o15347] 2849 Low confidence 204.627 201.172 1.01717
3203 High confidence 0.00001 0.00001 1
high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13] 2787
2853 Low confidence 204.574 201.124 1.01715
high-affinity cationic amino acid transporter-1 (cat-1) (cat1) (system y+ basic amino acid transporter) (ecotropic retroviral leukemia receptor homolog) (err) (ecotropic retrovirus receptor homolog). [swissprot;acc:p30825] 1095 200.661 195.999 1.02379
high-affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9a (ec 3.1.4.17). [swissprot;acc:o76083] 1138 187.917 183.608 1.02347
2876 High confidence 0.00001 0.00001 1
high-affinity copper uptake protein 1 (hctr1) (copper transporter 1). [swissprot;acc:o15431] 2783 Low confidence 203.964 200.475 1.0174
high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9] 2863 High confidence 0.00001 0.00001 1
4886 Low confidence 205.789 205.306 1.00235
high-mobility group 20a. [refseq;acc:nm_018200] 125 High confidence 208.588 171.778 1.21429
152 Low confidence 202.934 191.187 1.06144
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] 124 High confidence 208.52 171.595 1.21519
136 Low confidence 202.996 190.854 1.06362
highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] 440 High confidence 231.802 249.983 1.07843
3948 Low confidence 201.891 199.431 1.01234
hira protein (tup1 like enhancer of split protein 1). [swissprot;acc:p54198] 1976 196.815 193.041 1.01955
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] 409 149.423 144.256 1.03582
788 High confidence 138.705 132.538 1.04653
histidine ammonia-lyase (ec 4.3.1.3) (histidase). [swissprot;acc:p42357] 2168 Low confidence 198.997 195.273 1.01907
2169 High confidence 215.925 214.481 1.00673
histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] 1082 Low confidence 203.804 199.058 1.02384
1715 High confidence 206.549 203.844 1.01327
histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773] 24 Low confidence 188.298 228.509 1.21355
histidine-rich membrane protein ke4. [swissprot;acc:q92504] 2718 High confidence 216.52 216.632 1.00052
3336 Low confidence 200.629 197.551 1.01558
histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] 1271 192.956 188.71 1.0225
1920 High confidence 187.292 185.413 1.01013
histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] 1268 Low confidence 192.905 188.658 1.02251
1919 High confidence 187.231 185.349 1.01015
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 182 277.546 240.461 1.15422
908 Low confidence 203.746 198.738 1.0252
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 279 High confidence 252.644 228.42 1.10605
2118 Low confidence 200.802 197.017 1.01921
histone deacetylase 1 (hd1). [swissprot;acc:q13547] 777 High confidence 225.989 215.53 1.04853
2873 Low confidence 201.358 197.971 1.01711

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/