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 2551 to 2600 of 66312 in total
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Value Type
Interaction Map
red
green
network_comparison
160 DCHS1 protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0] Divided Rooted Low confidence 65.7817 70.2555 1.06801
FES proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Subtracted Ranked 216.783 205.066 11.717
GNAO1 guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Divided High confidence 249.663 298.263 1.19466
KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Subtracted Rooted 43.4291 31.7159 11.7132
MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Divided Measured 23693.7 18263 1.29736
MTHFR methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] Low confidence 10452.8 11320.8 1.08304
MYH7B dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Subtracted High confidence 9035 7279.6 1755.4
NEUROD6 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Ranked 312 284 28
PCSK5 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Divided Squared Low confidence 54208.6 48413.8 1.11969
PFKFB1 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 (6pf-2-k/fru- 2,6-p2ase liver isozyme) [includes: 6-phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:p16118] Subtracted 53380.6 47490 5890.6
161 APC2 adenomatous polyposis coli like. [refseq;acc:nm_005883] Divided Ranked 222.34 235.547 1.0594
CAPN2 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Subtracted Rooted 64.1536 68.7605 4.6069
DYNLT1 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Squared 53380.6 47490 5890.6
FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Ranked 219.6 207.907 11.693
HOXB4 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Divided Squared High confidence 173408 242989 1.40126
KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Subtracted Rooted 43.4519 31.7522 11.6997
MAGEF1 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Divided Measured 23693.7 18263 1.29736
MYH13 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Subtracted 9035 7279.6 1755.4
NEUROD1 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Ranked 312 284 28
PBLD mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] Divided Squared Low confidence 60522.9 67721 1.11893
RAP1GAP rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Ranked High confidence 249.663 298.263 1.19466
RPS6KC1 ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Subtracted Measured Low confidence 7020.48 7667.34 646.86
SLC15A2 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Divided Rooted 70.5717 75.371 1.06801
SLC16A5 monocarboxylate transporter 6 (mct 6) (mct 5). [swissprot;acc:o15375] Measured 10351.8 11210.8 1.08298
SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Rooted High confidence 52.7642 61.9019 1.17318
TRMU trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Subtracted Squared 52591.3 69845.1 17253.8
162 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Ranked 142 170 28
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Measured Low confidence 10519.4 9877.88 641.52
CLEC11A stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Squared High confidence 59704 76460.4 16756.4
DAD1 defender against cell death 1 (dad-1). [swissprot;acc:p46966] Divided Ranked Low confidence 197.99 186.913 1.05926
DAZAP1 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Subtracted Rooted 65.6112 70.2066 4.5954
FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Ranked 219.593 207.903 11.69
GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Divided Squared 53479.8 47812.1 1.11854
HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Subtracted Measured High confidence 5140.14 6893.53 1753.39
HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Divided Rooted 52.7642 61.9019 1.17318
HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Squared 173408 242989 1.40126
KCNIP2 kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] Subtracted Rooted 43.4554 31.7576 11.6978
MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] Divided Measured 23693.7 18263 1.29736
NOSTRIN nostrin. [refseq;acc:nm_052946] Ranked 209.299 249.187 1.19058
PFKFB2 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 (6pf-2-k/fru- 2,6-p2ase heart-type isozyme) (pfk-2/fbpase-2) [includes: 6- phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:o60825] Subtracted Squared Low confidence 53380.6 47490 5890.6
PSCD1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Divided Measured 12424.3 11472.3 1.08298
SEPT8 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Rooted 98.7481 105.459 1.06796
163 no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Squared High confidence 173408 242989 1.40126
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Measured 23693.7 18263 1.29736
ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Subtracted Ranked 133 105 28
CLEC3A c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Squared 59464 76120.8 16656.8
CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Divided Low confidence 56828 50808.5 1.11847
CSTF2T likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Subtracted Measured High confidence 14976.4 13246.6 1729.8
EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Divided Rooted 52.7702 61.8915 1.17285
NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Subtracted 54.935 66.6101 11.6751

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/