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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 380 to 429 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
95 SLC7A13 amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817] Subtracted Low confidence 200.497 185.679 14.818
96 ATF3 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] High confidence 201.949 153.671 48.278
MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Divided 88.2482 110.265 1.24949
SLC7A7 y+l amino acid transporter 1 (y(+)l-type amino acid transporter 1) (y+lat-1) (y+lat1) (monocyte amino acid permease 2) (mop-2). [swissprot;acc:q9um01] Low confidence 200.497 185.679 1.0798
Subtracted 14.818
97 APBA1 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] High confidence 271.752 225.68 46.072
MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Divided 88.2482 110.265 1.24949
SLC7A11 cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] Low confidence 200.497 185.679 1.0798
Subtracted 14.818
98 FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] High confidence 204.641 160.957 43.684
MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Divided 88.2482 110.265 1.24949
SLC7A6 solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] Low confidence 200.497 185.679 1.0798
Subtracted 14.818
99 no value jun dimerization protein. [refseq;acc:nm_130469] High confidence 204.641 160.957 43.684
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Divided 88.2482 110.265 1.24949
EIF4B eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] Low confidence 200.497 185.679 1.0798
Subtracted 14.818
100 FOSL2 fos-related antigen 2. [swissprot;acc:p15408] High confidence 204.641 161.046 43.595
MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Divided 88.2482 110.265 1.24949
SLC7A9 b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] Low confidence 200.497 185.679 1.0798
Subtracted 14.818
101 F13A1 coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] 226.395 211.713 14.682
FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] High confidence 204.641 161.051 43.59
MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Divided 88.2482 110.265 1.24949
ROGDI leucine zipper domain protein. [refseq;acc:nm_024589] Low confidence 221.996 238.82 1.07579
102 DGKQ diacylglycerol kinase, theta (ec 2.7.1.107) (diglyceride kinase) (dgk- theta) (dag kinase theta). [swissprot;acc:p52824] 229.556 213.456 1.07543
FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Subtracted High confidence 204.642 161.068 43.574
MAGED2 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Divided 88.2482 110.265 1.24949
TGM1 protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] Subtracted Low confidence 226.395 211.713 14.682
103 COL4A3BP goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] 220.969 235.572 14.603
JUNB transcription factor jun-b. [swissprot;acc:p17275] High confidence 201.144 158.868 42.276
PTPRA vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Divided Low confidence 203.948 189.652 1.07538
TRO trophinin. [swissprot;acc:q12816] High confidence 88.2482 110.265 1.24949
104 ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] Low confidence 219.277 204.212 1.07377
HOMER2 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] High confidence 252.371 202.016 1.24926
SLC11A1 natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] Subtracted Low confidence 225.666 211.107 14.559
TARDBP tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] High confidence 256.228 298.438 42.21
105 B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Low confidence 213.243 227.616 14.373
E2F1 transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Divided 220.497 205.364 1.07369
GNB1 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] High confidence 266.716 333.165 1.24914
JUND transcription factor jun-d. [swissprot;acc:p17535] Subtracted 200.941 158.941 42
106 COQ7 ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Divided 252.329 202.004 1.24913
DLGAP3 disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Subtracted Low confidence 197.731 212.069 14.338
E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Divided 220.497 205.364 1.07369
NOSTRIN nostrin. [refseq;acc:nm_052946] Subtracted High confidence 209.299 249.187 39.888
107 FAM89B mouse mammary turmor virus receptor homolog 1. [refseq;acc:nm_152832] Divided Low confidence 227.429 211.97 1.07293
HOMER1 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] High confidence 252.309 201.998 1.24907
PTPRA vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Subtracted Low confidence 203.948 189.652 14.296
SNF8 eap30 subunit of ell complex. [refseq;acc:nm_007241] High confidence 209.299 249.187 39.888
108 no value disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Low confidence 197.752 212.031 14.279

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/