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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 64574 to 64623 of 66312 in total
Interaction Map  : Low confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
4844 IBTK inhibitor of bruton's tyrsoine kinase; btk-binding protein. [refseq;acc:nm_015525] Measured Divided 8463.74 8544.71 1.00957
SH3GLB2 sh3-containing protein sh3glb2; sh3-domain, grb2-like, endophilin b2. [refseq;acc:nm_020145] Rooted Subtracted 70.9196 71.9002 0.9806
SLMO1 erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584] Ranked Divided 203.909 203.244 1.00327
4845 ARHGEF5 rho guanine nucleotide exchange factor 5 (guanine nucleotide regulatory protein tim) (oncogene tim) (p60 tim) (transforming immortalized mammary oncogene). [swissprot;acc:q12774] Measured 9065.96 8980.16 1.00955
CYP3A7 cytochrome p450 3a7 (ec 1.14.14.1) (cypiiia7) (p450-hfla). [swissprot;acc:p24462] Squared Subtracted 46592.3 46245.5 346.8
GNG12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Measured 6915.31 6990.74 75.43
KNG1 kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Rooted Divided 70.9553 71.9358 1.01382
OSBPL5 oxysterol binding protein-related protein 5 (osbp-related protein 5) (orp-5). [swissprot;acc:q9h0x9] Squared 45545.5 45920.5 1.00823
RAF1 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Ranked Subtracted 184.241 183.601 0.64
SH3GLB1 sh3-containing protein sh3glb1; sh3-containing protein sh3glb1; cgi-61 protein; endophilin b1; endophilin b1; bax-interacting factor 1; sh3-domain, grb2-like, endophilin b1. [refseq;acc:nm_016009] Rooted 70.9196 71.9002 0.9806
SLMO2 protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] Ranked Divided 203.909 203.244 1.00327
4846 ARAF a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Subtracted 184.234 183.595 0.639
BMP7 bone morphogenetic protein 7 precursor (bmp-7) (osteogenic protein 1) (op-1). [swissprot;acc:p18075] Squared Divided 44928.8 44566 1.00814
FABP7 fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540] Rooted 74.314 75.3405 1.01381
GADD45GIP1 papillomavirus l2 interacting nuclear protein 1; ckii beta binding protein 2; cr6 interacting factor 1; p53-responsive gene 6. [refseq;acc:nm_052850] Ranked 210.422 211.109 1.00326
GIPC1 rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Squared Subtracted 47739.8 48086.3 346.5
KNG1 kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Rooted 70.9553 71.9358 0.9805
LGTN ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Measured 7166.16 7240.99 74.83
SMAD2 mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796] Divided 8230.31 8308.86 1.00954
4847 no value intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Ranked 178.257 178.834 1.00324
BMP5 bone morphogenetic protein 5 precursor (bmp-5). [swissprot;acc:p22003] Squared 44917.8 44555.7 1.00813
CYP4A22 dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] Subtracted 47246.9 47589.6 342.7
HOOK2 hook2 protein. [refseq;acc:nm_013312] Measured Divided 8474.95 8555.81 1.00954
NUP107 nuclear pore complex protein nup107 (nucleoporin nup107) (107 kda nucleoporin). [swissprot;acc:p57740] Subtracted 8284.03 8358.63 74.6
PIGC phosphatidylinositol n-acetylglucosaminyltransferase subunit c (ec 2.4.1.198) (phosphatidylinositol-glycan biosynthesis, class c protein) (pig-c). [swissprot;acc:q92535] Rooted Divided 70.3657 71.3373 1.01381
POU3F2 pou domain, class 3, transcription factor 2 (nervous-system specific octamer-binding transcription factor n-oct-3) (brain-specific homeobox/pou domain protein 2) (brain-2) (brn-2 protein). [swissprot;acc:p20265] Subtracted 73.2993 74.2778 0.9785
ZNF394 zinc finger protein 99. [refseq;acc:nm_032164] Ranked 206.472 205.839 0.633
4848 no value myo-inositol 1-phosphate synthase a1. [refseq;acc:nm_016368] Divided 203.884 203.239 1.00317
pou domain, class 3, transcription factor 3 (brain-specific homeobox/pou domain protein 1) (brain-1) (brn-1 protein). [swissprot;acc:p20264] Rooted Subtracted 73.2993 74.2778 0.9785
BMP8A bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] Squared Divided 44910.2 44548.6 1.00812
FBXL11 f-box and leucine-rich repeat protein 11; f-box protein fbl11. [refseq;acc:nm_012308] Measured Subtracted 7399.95 7474.27 74.32
HOOK1 hook1 protein. [refseq;acc:nm_015888] Divided 8475.45 8556.21 1.00953
RPL5 60s ribosomal protein l5. [swissprot;acc:p46777] Rooted 69.0542 70.0063 1.01379
SDC3 syndecan-3 (synd3). [swissprot;acc:o75056] Squared Subtracted 53479.3 53139.6 339.7
ZSCAN12 zinc finger protein 305. [swissprot;acc:o43309] Ranked 206.479 205.846 0.633
4849 no value germ cell-less. [refseq;acc:nm_022471] 208.276 208.904 0.628
BMP6 bone morphogenetic protein 6 precursor (bmp-6). [swissprot;acc:p22004] Squared Divided 44916.6 44554.6 1.00812
COMP cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Measured Subtracted 7226.62 7300.69 74.07
CYP4A11 cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] Squared 47238 47576.6 338.6
HRBL hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] Measured Divided 8464.11 8544.68 1.00952
LARS2 probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] Rooted 76.1787 77.2177 1.01364
SPARCL1 sparc-like protein 1 precursor (high endothelial venule protein) (hevin) (mast 9). [swissprot;acc:q14515] Subtracted 73.2993 74.2778 0.9785
ZNF394 zinc finger protein 99. [refseq;acc:nm_032164] Ranked Divided 206.472 205.839 1.00308
4850 CYP3A5 cytochrome p450 3a5 (ec 1.14.14.1) (cypiiia5) (p450-pcn3). [swissprot;acc:p20815] Squared Subtracted 46609.5 46272.1 337.4
EIF1B protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Ranked 205.448 206.075 0.627
HOOK3 golgi-associated microtubule-binding protein hook3; hook3 protein. [refseq;acc:nm_032410] Measured Divided 8477.6 8557.97 1.00948
PHKG2 phosphorylase b kinase gamma catalytic chain, testis/liver isoform (ec 2.7.1.38) (phk-gamma-t) (phosphorylase kinase gamma subunit 2) (psk-c3). [swissprot;acc:p15735] Rooted 64.5419 63.6803 1.01353
SPARC sparc precursor (secreted protein acidic and rich in cysteine) (osteonectin) (on) (basement membrane protein bm-40). [swissprot;acc:p09486] Subtracted 73.2993 74.2778 0.9785
THBS3 thrombospondin 3 precursor. [swissprot;acc:p49746] Measured 7226.69 7300.73 74.04
XPO1 exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] Squared Divided 48323.1 47936 1.00808

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
- Hugo is the HGNC identifier if it exists
- 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/