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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2325 to 2374 of 77072 in total
Rank
description
Value Type
Network Comparison Type
Interaction Map
Filtered
red
green
network_comparison
73 phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] Ranked Divided High confidence 0 4119 5397 1.31027
platelet glycoprotein v precursor (gpv) (cd42d). [swissprot;acc:p40197] Squared Subtracted Low confidence 1 63279.9 51013.3 12266.6
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Measured Divided High confidence 0 65.2968 37.693 1.73233
rad50-interacting protein 1. [refseq;acc:nm_021930] Rooted Low confidence 1 64.6594 71.0277 1.09849
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Squared Subtracted High confidence 0 10596.4 8278.87 2317.53
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Measured 1965.47 2389.69 424.22
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Divided 1 4556.83 2945.38 1.54711
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Subtracted 22268.8 18560.4 3708.4
set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] Ranked Divided Low confidence 230.944 209.149 1.10421
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Measured 0 688.436 385.626 1.78524
transcription factor jun-b. [swissprot;acc:p17275] Ranked Subtracted 1 202.728 183.388 19.34
zinc finger protein 135. [swissprot;acc:p52742] Rooted 0 45.2856 40.6922 4.5934
74 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Squared High confidence 1 117858 70570.1 47287.9
arf gtpase-activating protein. [refseq;acc:nm_133446] Measured Divided Low confidence 0 66 37 1.78378
ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Ranked High confidence 6742.5 8759.5 1.29915
b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] Measured Low confidence 1 6991.78 7848.45 1.12253
bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] High confidence 0 501.151 859.34 1.71473
carboxypeptidase n 83 kda chain (carboxypeptidase n regulatory subunit) (fragment). [swissprot;acc:p22792] Squared Subtracted Low confidence 1 63279.6 51013.1 12266.5
diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] Rooted Divided 62.2472 68.3765 1.09847
dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] Squared Subtracted High confidence 0 18585 20796.3 2211.3
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] Divided Low confidence 600.627 1860.93 3.09831
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Ranked Subtracted High confidence 14548.5 11915.2 2633.3
dok-like protein. [refseq;acc:nm_024872] Rooted 5.91608 0 5.91608
glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] Squared Low confidence 33007.9 29539.6 3468.3
glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] Measured High confidence 14267.5 14688.8 421.3
high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9] Rooted Divided 5.01247 6.80523 1.35766
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Measured Subtracted 1 20446.1 24136.4 3690.3
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Rooted Low confidence 101.348 108.302 6.954
jumonji protein. [swissprot;acc:q92833] Ranked 0 22296.2 19621 2675.2
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Divided High confidence 1 288 362 1.25694
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Measured Subtracted Low confidence 11285.3 10318.5 966.8
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Rooted Divided High confidence 27.9136 37.2872 1.33581
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Ranked Low confidence 0 5900.08 7386.89 1.252
platelet glycoprotein v precursor (gpv) (cd42d). [swissprot;acc:p40197] Squared 1 63279.9 51013.3 1.24046
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Ranked Subtracted 225.428 244.701 19.273
protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0] Squared Divided High confidence 0 0.092781 0.0318343 2.9145
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Ranked Low confidence 1 195.817 215.516 1.1006
sedlin. [swissprot;acc:o14582] Rooted 0 8.7827 11.9458 1.36015
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] Measured High confidence 1 4556.99 2945.8 1.54694
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Ranked Subtracted 189.07 242.453 53.383
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Rooted 27.7254 44.0299 16.3045
trophinin. [swissprot;acc:q12816] Squared Divided 219048 129762 1.68808
zinc finger protein 195. [swissprot;acc:o14628] Measured Subtracted Low confidence 0 2353.86 1970.76 383.1
zinc finger protein 271 (zinc finger protein hzf7) (zinc finger protein znfphex133). [swissprot;acc:q14591] Rooted 45.2825 40.6891 4.5934
75 60s ribosomal protein l21. [swissprot;acc:p46778] Measured High confidence 572 992.083 420.083
adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] Ranked 8158 5530.5 2627.5
amiloride-sensitive sodium channel delta-subunit (epithelial na+ channel delta subunit) (delta enac) (nonvoltage-gated sodium channel 1 delta subunit) (scned) (delta nach). [swissprot;acc:p51172] Squared Divided Low confidence 5.89418 17.4184 2.95519
anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] Subtracted 1025.97 4491.06 3465.09
b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Divided 1 63087.3 50932.2 1.23865
Subtracted 12155.1

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/