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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Gene Rank description Value Type Network Comparison Type Filtered green red Interaction Map network_comparison
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
green
red
network_comparison
398 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Ranked 1 238.358 218.818 1.0893
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] Rooted 106.044 116.707 1.10055
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 0 15.2103 15.7266 1.03394
transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] Squared 386144 414704 1.07396
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Measured 1 5904.1 5084.26 1.16125
399 clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Ranked 226.226 207.889 1.08821
cyclin g2. [swissprot;acc:q16589] Rooted 106.044 116.707 1.10055
glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] Ranked 0 17271.4 16703.1 1.03402
intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Rooted 29.8694 30.8601 1.03317
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Squared 1 23222.8 18929.1 1.22683
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Measured 0 527.5 548.5 1.03981
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 1 4479.76 5201.41 1.16109
protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] Squared 0 110.672 103.239 1.072
400 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Measured 1 4479.76 5201.41 1.16109
cyclin g1 (cyclin g). [swissprot;acc:p51959] Rooted 106.044 116.707 1.10055
glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] Ranked 0 17278.4 16711 1.03395
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Squared 1 48419 39478.8 1.22646
mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683] Rooted 0 19.2528 19.8872 1.03295
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Measured 527.5 548.5 1.03981
phosducin-like protein (phlp). [swissprot;acc:q13371] Ranked 1 226.218 207.908 1.08807
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Squared 0 20652.4 19277.3 1.07133
401 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Measured 1 4479.76 5201.41 1.16109
axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Squared 40524.8 33044.3 1.22638
camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 0 4136.72 3862.64 1.07096
dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] Rooted 22.6039 21.8861 1.0328
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Measured 527.5 548.5 1.03981
replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] Ranked 1 226.218 207.908 1.08807
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Rooted 106.044 116.707 1.10055
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Ranked 0 11904.9 12305.9 1.03368
402 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Rooted 22.4088 21.6987 1.03273
adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5] Ranked 10918 10562.4 1.03367
brain protein 16. [refseq;acc:nm_016458] Squared 2371.77 2538.95 1.07049
endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] 1 48393.1 39472 1.22601
eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Rooted 55.2294 50.1918 1.10037
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Measured 4479.76 5201.41 1.16109
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 0 527.5 548.5 1.03981
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Ranked 1 226.218 207.908 1.08807
403 fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Measured 4479.76 5201.41 1.16109
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Squared 48362.1 39463.9 1.22548
ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] 0 1754.91 1872.12 1.06679
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Measured 527.5 548.5 1.03981
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Rooted 1 65.6741 59.6834 1.10037
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Ranked 226.218 207.908 1.08807
poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] Rooted 0 20.0671 19.4322 1.03267
udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795] Ranked 10111.2 9783.63 1.03348
404 40s ribosomal protein s3a. [swissprot;acc:p49241] Rooted 32.9781 34.0198 1.03159
adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Squared 1 32855.4 26819.1 1.22507
dna repair protein rad52 homolog. [swissprot;acc:p43351] Ranked 226.218 207.908 1.08807
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Measured 4479.76 5201.41 1.16109
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Rooted 65.6741 59.6834 1.10037

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/