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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 275 to 324 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Filtered
red
green
network_comparison
138 likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] 0 12384.7 10549.4 1.17397
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] 1 194.372 234.204 1.20493
139 alpha crystallin a chain. [swissprot;acc:p02489] 0 16372.4 13972.2 1.17178
amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] 1 271.752 225.68 1.20415
140 mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] 0 16411.9 14027.1 1.17001
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 1 59 49 1.20408
141 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 0 7690.02 8991.19 1.1692
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] 1 59 49 1.20408
142 ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 0 8214.41 7026.41 1.16908
143 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 1 59 49 1.20408
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] 0 11124.8 13005.3 1.16904
144 dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] 11123.4 13000.1 1.16872
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] 1 265.686 319.651 1.20312
145 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 265.639 319.546 1.20293
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 0 7955.61 6817.49 1.16694
146 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] 12577.8 14662.1 1.16571
kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] 1 265.632 319.531 1.20291
147 60s ribosomal protein l7. [swissprot;acc:p18124] 0 11080.3 9505.89 1.16562
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 1 50.7983 42.3003 1.2009
148 sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 296.677 247.559 1.19841
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] 0 6755.71 7863.63 1.164
149 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 1 142 170 1.19718
block 23. [sptrembl;acc:q8nhw5] 0 11469.3 13334.8 1.16265
150 myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] 1 55 46 1.19565
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] 0 8730 7516 1.16152
151 myosin vc (myosin 5c). [swissprot;acc:q9nqx4] 1 55 46 1.19565
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] 0 7502.08 6461.83 1.16098
152 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 1 55 46 1.19565
similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] 0 11438 13277.1 1.16079
153 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] 1 249.663 298.263 1.19466
tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] 0 7879.3 6789.92 1.16044
154 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 10883 12622.8 1.15986
regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] 1 249.663 298.263 1.19466
155 polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] 0 12759.4 11028.8 1.15692
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] 1 249.663 298.263 1.19466
156 regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081]
tubby protein homolog. [swissprot;acc:p50607] 0 12303.7 10641.7 1.15618
157 transcription factor lbx1. [swissprot;acc:p52954] 1 249.663 298.263 1.19466
transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] 0 18079 15652 1.15506
158 mosaic protein lgn. [swissprot;acc:p81274] 1 249.663 298.263 1.19466
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] 0 10060.2 11616.4 1.15469
159 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 5813.32 6706.32 1.15361
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] 1 249.663 298.263 1.19466
160 ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] 0 11732 13530.6 1.15331
guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] 1 249.663 298.263 1.19466
161 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 0 5781.93 6660.63 1.15197
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] 1 249.663 298.263 1.19466
162 nostrin. [refseq;acc:nm_052946] 209.299 249.187 1.19058
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] 0 12301.4 10680.5 1.15176

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/