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.


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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3930 to 3979 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
492 dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Squared 0 6791.15 6792.32 1.00017
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 1 5313 6389.9 1.20269
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Rooted 55.1759 60.2621 1.09218
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] 0 62.8936 62.8986 1.00008
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Measured 1 5979.94 6842.76 1.14429
serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] Ranked 220.171 235.979 1.0718
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] 0 6802.96 6829.74 1.00394
493 3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] Squared 17901.1 17901.1 1
cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Rooted 1 55.1759 60.2621 1.09218
conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] Ranked 220.172 235.98 1.0718
dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] 0 11999.1 12041.7 1.00355
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Rooted 62.8936 62.8986 1.00008
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Measured 1 5979.95 6842.78 1.14429
pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] 0 2410.35 2411.78 1.00059
serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549] Squared 1 28408.7 34148.5 1.20204
494 e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Measured 5979.93 6842.72 1.14428
electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] Squared 31583 37925.6 1.20082
histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261] Measured 0 0.00001 0.00001 1
Squared
Rooted
pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] 1 55.1759 60.2621 1.09218
serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Ranked 220.172 235.98 1.0718
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] 0 11985.5 11959.4 1.00218
495 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] 11725.2 11748.1 1.00195
60s ribosomal protein l8. [swissprot;acc:p25120] Rooted 1 55.1759 60.2621 1.09218
histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001] Measured 0 0.00001 0.00001 1
Squared
Rooted
partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Squared 1 30286.5 36362 1.2006
serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] Ranked 220.171 235.979 1.0718
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Measured 10804.7 12363.6 1.14428
496 hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] Rooted 55.1759 60.2621 1.09218
mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932] Measured 0 0.00001 0.00001 1
Squared
Rooted
nostrin. [refseq;acc:nm_052946] Measured 1 4682.87 4093.05 1.1441
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Ranked 250.938 234.134 1.07177
tubby protein homolog. [swissprot;acc:p50607] Squared 30286.5 36362 1.2006
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Ranked 0 9394 9411.49 1.00186
497 eap30 subunit of ell complex. [refseq;acc:nm_007241] Measured 1 4682.87 4093.05 1.1441
histone h2a; h2a histone family, member r. [refseq;acc:nm_170745] 0 0.00001 0.00001 1
Squared
Rooted
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Ranked 1 251.344 234.514 1.07177
protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] Squared 30286.5 36362 1.2006
pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Rooted 55.1759 60.2621 1.09218
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Ranked 0 13692.7 13718.2 1.00186
498 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 10231.8 10248.3 1.00161
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Measured 1 4682.87 4093.05 1.1441
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Squared 30286.5 36362 1.2006

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/