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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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 8241 to 8290 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1031 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Squared Divided 31994 36719.6 1.1477
hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] Ranked Subtracted 219.01 212.468 6.542
kappa b-ras 1. [refseq;acc:nm_020345] Rooted Divided 61.2289 64.4564 1.05271
membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] Measured 6136.99 6714.98 1.09418
peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] Subtracted 6437.99 6969.67 531.68
prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] Squared 26925.7 30311.3 3385.6
probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] Ranked Divided 242.978 235.518 1.03167
t-cell activation wd repeat protein. [refseq;acc:nm_139281] Rooted Subtracted 51.7169 55.044 3.3271
1032 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] Ranked Divided 186.664 180.943 1.03162
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Squared 31994 36719.6 1.1477
heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652] Measured Subtracted 6437.99 6969.67 531.68
i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] Rooted Divided 61.2289 64.4564 1.05271
pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399] Squared Subtracted 26925.7 30311.3 3385.6
prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] Rooted 57.5529 60.879 3.3261
ran binding protein 11. [refseq;acc:nm_016338] Measured Divided 6138.91 6717.05 1.09418
vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606] Ranked Subtracted 219.01 212.468 6.542
1033 asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]
disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] Squared Divided 31994 36719.6 1.1477
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Measured 6080.91 6653.52 1.09417
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Subtracted 6437.99 6969.67 531.68
inositol polyphosphate multikinase. [refseq;acc:nm_152230] Squared 22271.9 25656.8 3384.9
prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212] Rooted 57.5529 60.879 3.3261
snare associated protein snapin. [refseq;acc:nm_012437] Divided 61.2289 64.4564 1.05271
tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] Ranked 221.183 214.406 1.03161
1034 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] Subtracted 229.442 235.974 6.532
afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6] Squared 22271.9 25656.8 3384.9
heat shock cognate 71 kda protein. [swissprot;acc:p11142] Measured 6437.99 6969.67 531.68
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Squared Divided 31994 36719.6 1.1477
s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266] Measured 6152.88 6732.12 1.09414
steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Ranked 186.551 180.837 1.0316
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Rooted Subtracted 54.6759 51.3516 3.3243
transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] Divided 58.8683 61.9622 1.05256
1035 alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [swissprot;acc:q9byc5] Squared Subtracted 22271.9 25656.8 3384.9
atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301] Ranked Divided 221.682 228.68 1.03157
beta-catenin (pro2286). [swissprot;acc:p35222] Measured Subtracted 5635.26 6166.09 530.83
c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Rooted Divided 60.6801 63.8644 1.05248
casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730] Measured 5054.73 5530.23 1.09407
limkain b1. [refseq;acc:nm_019081] Squared 31994 36719.6 1.1477
ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] Ranked Subtracted 229.441 235.972 6.531
tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] Rooted 54.6759 51.3516 3.3243
1036 atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] 51.6795 54.9937 3.3142
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Squared 20305.9 23689.4 3383.5
coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] Ranked Divided 171.341 176.746 1.03155
dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622] Subtracted 207.719 214.236 6.517
fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] Measured Divided 6077.65 6649.22 1.09404
putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Squared 31994 36719.6 1.1477
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Measured Subtracted 5910.54 6440.58 530.04
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Rooted Divided 60.6801 63.8644 1.05248
1037 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] Squared 31994 36719.6 1.1477
cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] Rooted Subtracted 51.7273 55.0399 3.3126

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/