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 4508 to 4557 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
564 ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Ranked Subtracted 220.744 207.121 13.623
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Rooted Divided 62.7424 67.9648 1.08324
sprouty homolog 3 (spry-3). [swissprot;acc:o43610] Squared Subtracted 27174.1 31992.4 4818.3
tbc1 domain family member 5. [swissprot;acc:q92609] Measured 6374.65 7145.59 770.94
transforming protein rhoa (h12). [swissprot;acc:p06749] Divided 5480.24 6222.04 1.13536
565 calcyphosine. [swissprot;acc:q13938] Ranked Subtracted 220.744 207.121 13.623
fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] Squared Divided 25287.7 30003.7 1.18649
limkain b1. [refseq;acc:nm_019081] Rooted 62.7424 67.9648 1.08324
sedlin. [swissprot;acc:o14582] Ranked 129.219 121.261 1.06563
small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] Measured 10434.4 11846.2 1.1353
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] Rooted Subtracted 55.5489 50.535 5.0139
sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] Squared 27174.1 31992.4 4818.3
tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Measured 6374.65 7145.59 770.94
566 autoantigen ngp-1. [swissprot;acc:q13823] Divided 3766.14 4274.79 1.13506
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Rooted Subtracted 55.5489 50.535 5.0139
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Ranked 220.744 207.121 13.623
putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Rooted Divided 62.7424 67.9648 1.08324
sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Squared Subtracted 27174.1 31992.4 4818.3
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Ranked Divided 129.219 121.261 1.06563
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Squared 34268.1 40650.4 1.18625
vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Measured Subtracted 6374.65 7145.59 770.94
567 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] Ranked 228.639 242.258 13.619
bet3 homolog. [swissprot;acc:o43617] Divided 129.219 121.261 1.06563
cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] Rooted 62.7424 67.9648 1.08324
deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Measured 10264.9 9043.51 1.13506
glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [swissprot;acc:p06744] Squared Subtracted 29924.3 34690.9 4766.6
methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Rooted 61.2527 66.2644 5.0117
numb-like protein (numb-r). [swissprot;acc:q9y6r0] Measured 6374.65 7145.59 770.94
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Squared Divided 34219.8 40585.4 1.18602
568 cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708] Subtracted 25396.2 30143.4 4747.2
disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Rooted Divided 62.7424 67.9648 1.08324
grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] Measured 4134.77 4691.24 1.13458
max protein. [swissprot;acc:p25912] Squared 18764.5 22255 1.18602
putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] Ranked 226.3 212.38 1.06554
splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955] Subtracted 228.639 242.258 13.619
tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Measured 6374.65 7145.59 770.94
u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] Rooted 59.7823 64.7895 5.0072
569 40s ribosomal protein s29. [swissprot;acc:p30054] 50.2784 45.294 4.9844
amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203] Ranked 228.639 242.258 13.619
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Squared 25294.9 30027.4 4732.5
grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7] Measured Divided 4134.77 4691.24 1.13458
kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Rooted 62.7424 67.9648 1.08324
t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] Squared 52623.3 44380.3 1.18574
t54 protein. [swissprot;acc:q92917] Ranked 226.3 212.38 1.06554
vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Measured Subtracted 6374.65 7145.59 770.94
570 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Rooted Divided 62.7424 67.9648 1.08324
double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] Squared 52623.3 44380.3 1.18574
ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Subtracted 31999.3 36726.8 4727.5
protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Measured 6374.65 7145.59 770.94
sorting nexin 17. [swissprot;acc:q15036] Ranked 228.639 242.258 13.619

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/