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 4708 to 4757 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
589 nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Measured Divided 6739.85 7644.63 1.13424
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Ranked Subtracted 217.67 230.596 12.926
rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423] Squared Divided 23526.4 27879.3 1.18502
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Ranked 228.215 214.546 1.06371
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Measured Subtracted 6691.21 7444.22 753.01
590 15 kda selenoprotein precursor. [swissprot;acc:o60613] Squared 29772.1 34456.5 4684.4
60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Rooted 50.3169 45.4333 4.8836
intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Ranked 217.67 230.596 12.926
oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8] Squared Divided 23526.4 27879.3 1.18502
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Ranked 217.215 204.279 1.06333
similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] Measured 6739.85 7644.63 1.13424
transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Rooted 108.671 100.365 1.08276
ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] Measured Subtracted 6690.44 7443.29 752.85
591 choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329] Squared Divided 23526.5 27879.4 1.18502
hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] Ranked Subtracted 217.67 230.596 12.926
homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Measured Divided 6740.5 7644.76 1.13415
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Squared Subtracted 15482.3 20162.4 4680.1
leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Rooted Divided 108.659 100.356 1.08274
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Subtracted 54.4927 49.6125 4.8802
ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] Ranked Divided 216.72 230.439 1.0633
u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] Measured Subtracted 5390.78 6142.07 751.29
592 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Rooted 54.4927 49.6125 4.8802
arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] Squared 31783.9 36463.3 4679.4
arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] Measured 7093.86 7842.67 748.81
cgthba protein (-14 gene protein). [swissprot;acc:q12980] Ranked 217.67 230.596 12.926
histone h2b.c (h2b/c). [swissprot;acc:q99880] Measured Divided 3946.32 4475.47 1.13409
protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Ranked 91.63 97.4011 1.06298
ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Rooted 108.659 100.356 1.08274
voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303] Squared 23526.4 27879.3 1.18502
593 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Rooted Subtracted 54.4927 49.6125 4.8802
aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] Squared Divided 23526.4 27879.3 1.18502
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Measured 3946.32 4475.47 1.13409
hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Ranked Subtracted 217.67 230.596 12.926
nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Measured 6770.78 7517.97 747.19
protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] Squared 31010.8 35677.6 4666.8
tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] Ranked Divided 232.118 218.406 1.06278
transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Rooted 108.653 100.352 1.08272
594 histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Measured 3946.32 4475.47 1.13409
importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] Squared 23517.1 27867.3 1.18498
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Rooted Subtracted 54.4927 49.6125 4.8802
pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Ranked Divided 223.282 210.136 1.06256
protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Squared Subtracted 30999.6 35666.3 4666.7
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Ranked 207.26 194.346 12.914
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Measured 6089.21 6835.34 746.13
transforming protein n-ras. [swissprot;acc:p01111] Rooted Divided 108.65 100.35 1.08271
595 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Squared 34129.7 40434.8 1.18474
6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] Subtracted 29345.7 34004.2 4658.5
apical-like protein (apxl protein). [swissprot;acc:q13796] Measured 6088.77 6834.87 746.1
fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Rooted 54.4927 49.6125 4.8802
fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Divided 51.2427 55.468 1.08246

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/