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 4858 to 4907 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
304 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Measured Divided 1 4855.46 5824.52 1.19958
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Squared 28896.2 36767 1.27238
rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] Rooted 0 31.3568 29.2362 1.07253
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Subtracted 1 53.6107 61.5862 7.9755
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Ranked Divided 0 8021.78 7496.8 1.07003
transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] Measured Subtracted 334.012 420.355 86.343
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Divided 4962.34 5469.68 1.10224
305 40s ribosomal protein s29. [swissprot;acc:p30054] Squared 5295.67 6326.82 1.19472
atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Rooted Subtracted 1 75.6323 67.6572 7.9751
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Measured 0 293.178 379.474 86.296
cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Rooted Divided 1 203.673 182.638 1.11517
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] Subtracted 0 25.2821 26.9306 1.6485
ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] Divided 24.6278 26.4005 1.07198
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Ranked Subtracted 1 88.2482 110.265 22.0168
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 0 16321 15577 744
microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650] Divided 9431 8815 1.06988
mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] 1 242.339 266.986 1.1017
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Squared Subtracted 28918.3 36746 7827.7
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Measured Divided 3856.29 4624.15 1.19912
paxillin. [swissprot;acc:p49023] Subtracted 5221.28 6314.35 1093.07
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Squared Divided 28896.2 36767 1.27238
sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Measured 0 4962.34 5469.68 1.10224
transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] Squared Subtracted 158.413 229.842 71.429
306 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Ranked Divided 1 242.153 266.673 1.10126
cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Measured Subtracted 0 293.178 379.474 86.296
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] Divided 1705.19 1547.2 1.10211
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Ranked Subtracted 1 88.2482 110.265 22.0168
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Measured 8430.03 9518.11 1088.08
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Ranked 0 16321 15577 744
microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650] Rooted 17.4356 19.0526 1.617
ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Squared 1 33044.9 40781.4 7736.5
pnas-18. [sptrembl;acc:q9bzu3] Measured Divided 13680.5 11409.6 1.19903
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Squared 28896.2 36767 1.27238
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Subtracted 0 61.6678 132.922 71.2542
rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Rooted Divided 1 56.3935 62.8817 1.11505
scribble. [refseq;acc:nm_015356] 0 18.8966 17.6385 1.07133
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Subtracted 1 127.967 120.003 7.964
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Squared Divided 0 31.0895 37.1241 1.1941
williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71] Ranked 5540 5921 1.06877
307 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] Measured Subtracted 1 7556.75 8636.87 1080.12
60s ribosomal protein l7. [swissprot;acc:p18124] Squared Divided 0 5826.27 6955.21 1.19377
aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] Subtracted 1 33010.8 40732.2 7721.4
ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] Ranked Divided 0 1091 1021 1.06856
cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Measured Subtracted 292.152 378.206 86.054
ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Divided 4159.87 3775.43 1.10183
grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Squared 1 28896.4 36766.8 1.27237
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Rooted 0 53.5229 49.96 1.07132
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Ranked Subtracted 1 88.2482 110.265 22.0168
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 0 16321 15577 744
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Rooted 1 66.0989 74.0609 7.962

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/