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 Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 6408 to 6457 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
green
red
network_comparison
401 mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932] Ranked Subtracted 0 20558 20914 356
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] 1 236.224 254.434 18.21
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Measured Divided 0 527.5 548.5 1.03981
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Squared Subtracted 1 33982.7 28188.7 5794
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 Divided 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
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] Squared Subtracted 0 5.42219 12.5892 7.16701
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Ranked Divided 11904.9 12305.9 1.03368
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Rooted Subtracted 1 62.0565 55.9231 6.1334
402 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Divided 0 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
Subtracted 355.6
arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] Measured 1 7168.2 6230.94 937.26
brain protein 16. [refseq;acc:nm_016458] Squared Divided 0 2371.77 2538.95 1.07049
cab2. [refseq;acc:nm_033419] Subtracted 7.16592 0 7.16592
endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Divided 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
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Squared Subtracted 33984.1 28190.4 5793.7
highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] Ranked 249.983 231.802 18.181
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Measured Divided 4479.76 5201.41 1.16109
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Subtracted 0 39.8063 12.6208 27.1855
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Divided 527.5 548.5 1.03981
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Rooted Subtracted 1 65.604 59.5128 6.0912
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Ranked Divided 226.218 207.908 1.08807
uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452] Rooted Subtracted 0 17.1002 17.8274 0.7272
403 beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] Squared 1 33984.1 28190.4 5793.7
calcyphosine. [swissprot;acc:q13938] Rooted 65.604 59.5128 6.0912
fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Measured Divided 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
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Rooted Subtracted 0 14.7645 15.4896 0.7251
ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] Squared Divided 1754.91 1872.12 1.06679
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] Measured Subtracted 2264.37 2290.09 25.72
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Ranked 1 246.338 228.468 17.87
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Measured Divided 0 527.5 548.5 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
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Measured Subtracted 1 7190.91 6259.3 931.61
protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] Squared 0 87.5656 94.678 7.1124
scribble. [refseq;acc:nm_015356] Ranked 12719 12370.5 348.5
udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795] Divided 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
alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] Subtracted 33984.1 28190.4 5793.7
bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] Ranked 246.33 228.463 17.867
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Rooted 65.604 59.5128 6.0912
dna repair protein rad52 homolog. [swissprot;acc:p43351] Ranked Divided 226.218 207.908 1.08807
dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] Squared Subtracted 0 3221.55 3228.32 6.77
importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Measured 1 8731.82 7802.31 929.51
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Divided 4479.76 5201.41 1.16109

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/