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 [...,...].
Gene Rank description Value Type Network Comparison Type Interaction Map green red Filtered 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
green
red
Filtered
network_comparison
398 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Ranked 238.358 218.818 1 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] 15.2103 15.7266 0 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 5904.1 5084.26 1 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 17271.4 16703.1 0 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 23222.8 18929.1 1 1.22683
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Measured 527.5 548.5 0 1.03981
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 4479.76 5201.41 1 1.16109
protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] Squared 110.672 103.239 0 1.072
400 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Measured 4479.76 5201.41 1 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 17278.4 16711 0 1.03395
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Squared 48419 39478.8 1 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 19.2528 19.8872 0 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 226.218 207.908 1 1.08807
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Squared 20652.4 19277.3 0 1.07133
401 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Measured 4479.76 5201.41 1 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] 4136.72 3862.64 0 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 226.218 207.908 1 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 11904.9 12305.9 0 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] 48393.1 39472 1 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] 527.5 548.5 0 1.03981
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Ranked 226.218 207.908 1 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] 1754.91 1872.12 0 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 65.6741 59.6834 1 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 20.0671 19.4322 0 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 32855.4 26819.1 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/