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 651 to 700 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
41 nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] Measured Divided 0 266 645 2.42481
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Ranked 1 322 253 1.27273
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Rooted Subtracted 60.8365 77.7233 16.8868
spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] 0 42.8135 51.3517 8.5382
suppressor of actin 1. [refseq;acc:nm_014016] Divided 3.30572 5.87091 1.77599
trophinin. [swissprot;acc:q12816] Measured Subtracted 1 23693.7 18263 5430.7
42 acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] Rooted Divided 0 5.11118 9.0312 1.76695
adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] Ranked 8158 5530.5 1.47509
cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Squared Subtracted 1 211446 137422 74024
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Ranked 0 9429.18 5208.84 4220.34
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Measured 1 21785.2 16426.1 5359.1
guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Divided 1857.32 958.237 1.93827
Rooted 40.225 24.7051 1.62821
jun dimerization protein. [refseq;acc:nm_130469] Subtracted 60.8365 77.7233 16.8868
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Squared Divided 144911 81154.7 1.78561
nanos (fragment). [sptrembl;acc:q8wy41] 0 33.64 5.39669 6.23345
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] Measured 205.439 86.9525 2.36266
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Ranked 1 204.641 160.957 1.2714
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Rooted Subtracted 0 90.4079 98.9265 8.5186
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] Squared 36765.6 31220.1 5545.5
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Ranked 1 332.874 267.246 65.628
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Measured 0 18889 19496 607
43 40s ribosomal protein s26. [swissprot;acc:p02383] Rooted Divided 9.92134 5.66499 1.75134
apg3p; pc3-96 protein. [refseq;acc:nm_022488] Measured Subtracted 1 21785.2 16426.1 5359.1
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Squared Divided 144876 81136.5 1.78558
dok-like protein. [refseq;acc:nm_024872] Ranked Subtracted 0 17571 21783 4212
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Measured Divided 263.66 587.988 2.2301
fos-related antigen 2. [swissprot;acc:p15408] Rooted Subtracted 1 60.8675 77.7168 16.8493
glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Ranked Divided 0 12143.8 8356.02 1.4533
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Rooted 1 40.6302 25.4452 1.59677
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Measured 1881.02 1027.36 1.83093
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Squared Subtracted 0 84951.4 90481 5529.6
jun dimerization protein. [refseq;acc:nm_130469] Ranked Divided 1 204.641 160.957 1.2714
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Subtracted 332.874 267.246 65.628
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Squared 110342 184298 73956
nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] Divided 0 16.747 98.4675 5.87971
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Measured Subtracted 4089.65 4696.36 606.71
zinc finger protein 277. [swissprot;acc:q9nrm2] Rooted 90.4079 98.9265 8.5186
44 acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] Measured Divided 45.4292 98.5074 2.16837
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Subtracted 1 28136.5 33457.6 5321.1
fos-related antigen 2. [swissprot;acc:p15408] Ranked Divided 204.641 161.046 1.2707
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Squared 139741 78454.6 1.78117
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Rooted 0 11.9583 6.85565 1.7443
glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] Ranked Subtracted 15863.6 11662.3 4201.3
guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Rooted Divided 1 40.5691 25.4263 1.59556
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Measured 1931.34 1057.39 1.82652
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Ranked Subtracted 332.874 267.246 65.628
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Squared 110342 184298 73956
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Rooted 60.8692 77.7165 16.8473
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] 0 33.5215 25.0836 8.4379

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/