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 2977 to 3026 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
373 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] Ranked Divided 242.37 265.255 1.09442
arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] Squared Subtracted 28863.2 35031.5 6168.3
band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] Divided 45986 56776.1 1.23464
dynactin 4. [refseq;acc:nm_032486] Ranked Subtracted 233.142 252.253 19.111
guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Rooted Divided 49.3451 54.4606 1.10367
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Subtracted 61.3354 67.8621 6.5267
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Measured Divided 5066.99 5926.1 1.16955
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Subtracted 4682.88 5646.19 963.31
374 60s ribosomal protein l26. [swissprot;acc:q02877] Rooted Divided 50.2549 45.5599 1.10305
e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Subtracted 61.3352 67.8618 6.5266
electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117] Squared 31189.6 37352.8 6163.2
homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Measured 4246.95 5208.98 962.03
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Ranked 248.152 267.226 19.074
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Measured Divided 5066.93 5925.38 1.16942
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] Squared 45987 56777.1 1.23463
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Ranked 267.208 244.168 1.09436
375 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] Squared 45987 56777.1 1.23463
60s ribosomal protein l35. [swissprot;acc:p42766] Rooted 50.2545 45.5637 1.10295
adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Ranked Subtracted 248.152 267.226 19.074
dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] Divided 242.686 265.516 1.09407
rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Rooted Subtracted 56.3935 62.8817 6.4882
u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Measured Divided 4700.42 5492.63 1.16854
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Subtracted 4250.14 5211.25 961.11
ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] Squared 29547.4 35683.5 6136.1
376 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Rooted Divided 50.2554 45.5688 1.10285
44050 protein. [refseq;acc:nm_178832] Measured 17385.9 14889.2 1.16769
adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Ranked Subtracted 248.152 267.226 19.074
galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Squared Divided 46021.4 56813.2 1.2345
growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] Rooted Subtracted 61.2684 67.755 6.4866
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Measured 4251.65 5212.33 960.68
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Ranked Divided 257.017 234.945 1.09395
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Squared Subtracted 29544.1 35678.3 6134.2
377 dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] Ranked Divided 242.691 265.481 1.09391
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Measured Subtracted 4252.66 5213.05 960.39
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Ranked 248.152 267.226 19.074
mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Rooted Divided 50.2554 45.5687 1.10285
nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] Measured 17385.9 14889.2 1.16769
ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Squared 33044.9 40781.4 1.23412
serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] Rooted Subtracted 61.2684 67.755 6.4866
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] Squared 29540.4 35672.6 6132.2
378 60s ribosomal protein l30. [swissprot;acc:p04645] Ranked Divided 242.593 265.365 1.09387
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Squared 15034.5 18552.2 1.23398
fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Ranked Subtracted 248.152 267.226 19.074
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Measured Divided 12471.7 14561.7 1.16758
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Rooted 50.5816 45.8738 1.10263
partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Squared Subtracted 30286.5 36362 6075.5
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Rooted 47.3621 53.8355 6.4734
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Measured 6272.91 7226.06 953.15
379 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] Ranked Divided 241.509 264.163 1.0938
aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] Squared 33010.8 40732.2 1.23391

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/