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 Filtered Network Comparison Type Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 3632 to 3681 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
description
Rank
Filtered
red
green
network_comparison
voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 80 1 254.691 202.668 1.25669
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 81 254.614 202.646 1.25645
142 0 8214.41 7026.41 1.16908
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] 78 1 254.693 202.668 1.2567
voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722] 1956 211.633 213.703 1.00978
voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303] 1968
voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448] 1954 211.632 1.00979
vps28 protein homolog. [swissprot;acc:q9uk41] 2871 0.00001 0.00001 1
wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [refseq;acc:nm_020830] 1407 206.104 210.424 1.02096
wd repeat domain 26. [refseq;acc:nm_025160] 1429 213.351 217.74 1.02057
wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950] 1410 206.1 210.417 1.02095
wd-repeat containing protein ciao 1. [swissprot;acc:o76071] 2927 0.00001 0.00001 1
wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] 507 251.299 234.729 1.07059
wd-repeat protein 3. [swissprot;acc:q9unx4] 912 243.896 234.96 1.03803
wd-repeat protein 4. [swissprot;acc:p57081] 2217 221.509 220.108 1.00637
wd-repeat protein bing4. [swissprot;acc:o15213] 1008 243.227 235.475 1.03292
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] 853 108.289 112.772 1.0414
werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] 1325 217.133 212.289 1.02282
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] 458 0 16416.1 16721.6 1.01861
1876 1 223.862 226.271 1.01076
williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044] 457 0 16416.1 16721.6 1.01861
1875 1 223.862 226.271 1.01076
williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71] 306 0 5540 5921 1.06877
3218 1 0.00001 0.00001 1
williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] 456 0 16416.1 16721.6 1.01861
1874 1 223.862 226.271 1.01076
wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007] 2625 204.304 204.028 1.00135
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 546 207.222 194.262 1.06671
wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [swissprot;acc:q92558] 1975 214.611 212.546 1.00972
wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [swissprot;acc:q9y6w5] 1973
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] 273 0 12748.1 11770.9 1.08302
1974 1 214.611 212.546 1.00972
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] 825 206.214 197.614 1.04352
wnt1 inducible signaling pathway protein 1 isoform 1 precursor; wnt-1 signaling pathway protein 1; wnt1 signaling pathway protein 1; wnt-1 inducible signaling pathway protein 1. [refseq;acc:nm_003882] 3109 0.00001 0.00001 1
wnt1 inducible signaling pathway protein 3 isoform 1; wnt-1 signaling pathway protein 3; wnt1 signaling pathway protein 3; wnt-1 inducible signaling pathway protein 3. [refseq;acc:nm_003880] 3065
ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] 1537 228.419 232.376 1.01732
ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] 1073 216.901 210.485 1.03048
xanthine dehydrogenase/oxidase [includes: xanthine dehydrogenase (ec 1.1.1.204) (xd); xanthine oxidase (ec 1.1.3.22) (xo) (xanthine oxidoreductase)]. [swissprot;acc:p47989] 2882 0.00001 0.00001 1
xap-5 protein (hxc-26 protein). [swissprot;acc:q14320] 1685 216.899 213.889 1.01407
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] 856 215.028 206.623 1.04068
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 9 212 309 1.45755
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] 738 222.825 211.966 1.05123
xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] 2328 209.326 208.357 1.00465
xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108] 2476 211.205 210.577 1.00298
yeast sec31p homolog. [refseq;acc:nm_014933] 1136 218.484 212.675 1.02731
yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470] 1955 211.633 213.703 1.00978
yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906] 1639 194.516 197.364 1.01464
yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] 528 222.146 237.393 1.06864
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] 1626 217.446 214.2 1.01515
zasp protein (fragment). [sptrembl;acc:q9y4z3] 1992 219.267 217.207 1.00948

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/