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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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 5962 to 6011 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
373 myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Ranked Subtracted 0 8125.5 7697.5 428
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Rooted 1 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
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Rooted 0 30.3054 31.5389 1.0407
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Squared 215.107 192.635 1.11666
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Measured Subtracted 3219.3 3174.79 44.51
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] 1 4682.88 5646.19 963.31
374 60s ribosomal protein l26. [swissprot;acc:q02877] Rooted Divided 50.2549 45.5599 1.10305
adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] Measured 0 2323.8 2452.23 1.05527
alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Squared 2572.14 2869.96 1.11579
calcyphosine. [swissprot;acc:q13938] Ranked 9874.54 9478.1 1.04183
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Measured Subtracted 100 144 44
e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Rooted 1 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
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Ranked 0 8125.5 7697.5 428
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 1 248.152 267.226 19.074
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Rooted Divided 0 30.2858 31.5117 1.04048
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Measured 1 5066.93 5925.38 1.16942
serpin b11. [swissprot;acc:q96p15] Rooted Subtracted 0 6.48074 7.48331 1.00257
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] Squared Divided 1 45987 56777.1 1.23463
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Subtracted 0 215.107 192.635 22.472
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Ranked Divided 1 267.208 244.168 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
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] Rooted 0 6.48074 7.48331 1.00257
dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] Ranked Divided 1 242.686 265.516 1.09407
estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] Measured 0 2323.8 2452.23 1.05527
germ cell-less. [refseq;acc:nm_022471] Rooted 27.8491 26.7806 1.0399
importin 9. [refseq;acc:nm_018085] Squared 1062.18 952.74 1.11487
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] Subtracted 80.1214 102.556 22.4346
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Ranked 8125.5 7697.5 428
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Measured 187 144 43
rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Rooted 1 56.3935 62.8817 6.4882
tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975] Ranked Divided 0 14247.6 13686.9 1.04097
u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Measured 1 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 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] Rooted Divided 0 32.3671 31.1453 1.03923
40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 1 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
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Ranked 0 8125.5 7697.5 428
myosin vi. [swissprot;acc:q9um54] Squared 39.56 17.2035 22.3565
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] Divided 1062.18 952.74 1.11487
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Ranked 1 257.017 234.945 1.09395

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/