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 630 to 679 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Filtered
red
green
network_comparison
315 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 0 12121.6 12887.6 1.06319
316 dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] 10768.5 11444 1.06273
protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] 1 242.694 267.017 1.10022
317 protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] 0 19939 18778 1.06183
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 1 224.445 204.044 1.09998
318 mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] 242.011 266.18 1.09987
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] 0 8918.54 9465.32 1.06131
319 60s ribosomal protein l19. [swissprot;acc:p14118] 1 240.73 264.729 1.09969
sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] 0 8918.54 9465.32 1.06131
320 adp-ribosylation factor 3. [swissprot;acc:p16587] 11627.8 10958.2 1.0611
epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] 1 241.892 265.96 1.0995
321 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] 0 11634.4 10989.9 1.05864
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 1 241.892 265.959 1.09949
322 deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 86.7483 78.8995 1.09948
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] 0 11634.4 10989.9 1.05864
323 60s ribosomal protein l23a. [swissprot;acc:p29316] 1 241.884 265.945 1.09947
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] 0 17387.1 16427.3 1.05843
324 40s ribosomal protein s23. [swissprot;acc:p39028] 1 243.944 268.195 1.09941
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] 0 17387.1 16427.3 1.05843
325 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] 1 243.944 268.195 1.09941
mstp028 protein. [refseq;acc:nm_031954] 0 7965.66 7528.21 1.05811
326 60s ribosomal protein l5. [swissprot;acc:p46777] 1 241.899 265.924 1.09932
dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] 0 11948.4 11295.6 1.05779
327 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 9897.29 10466.5 1.05751
dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] 1 243.817 267.962 1.09903
328 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 258.437 235.183 1.09888
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] 0 10897 11520 1.05717
329 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] 1 312 284 1.09859
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] 0 15977.3 15115.5 1.05701
330 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] 1 312 284 1.09859
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] 0 12320.2 13018.5 1.05668
331 40s ribosomal protein s3a. [swissprot;acc:p49241] 10405.1 10992.4 1.05644
doc-1 related protein (doc-1r). [swissprot;acc:o75956] 1 312 284 1.09859
332 myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 0 8125.5 7697.5 1.0556
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] 1 312 284 1.09859
333 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 0 8125.5 7697.5 1.0556
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 1 312 284 1.09859
334 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] 0 8125.5 7697.5 1.0556
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 1 312 284 1.09859
335 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 0 8125.5 7697.5 1.0556
336 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] 1 312 284 1.09859
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 0 8125.5 7697.5 1.0556
337 60s ribosomal protein l12. [swissprot;acc:p30050] 1 243.583 267.527 1.0983
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] 0 12953.2 12273.2 1.05541
338 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 1 243.583 267.528 1.0983
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] 0 11149.7 10571.4 1.0547
339 dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 1 243.583 267.527 1.0983
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] 0 10344.1 10903.3 1.05406
340 guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 11372.3 10792.3 1.05374

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/