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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Network Comparison Type Value Type Gene description Rank green network_comparison red Filtered Interaction Map
Results: HTML CSV LaTeX Showing element 368 to 417 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
description
Rank
green
network_comparison
red
b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] 1556 192.996 1.01656 196.192
b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 980 134.713 1.03396 130.289
b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 181 267.265 1.16294 229.818
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 244 254.15 1.11785 227.357
ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] 464 226.764 1.07686 210.578
ba203i16.1 (hypothetical protein kiaa0970). [sptrembl;acc:q9h1w1] 3117 0.00001 1 0.00001
ba207c16.2 (fragment). [sptrembl;acc:q9nql7] 2599 211.361 1.00142 211.662
ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] 2148 219.366 1.00686 217.871
ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] 2115 213.14 1.007 214.632
ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] 931 164.917 1.03637 159.13
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 452 207.972 1.07784 224.161
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 1568 224.767 1.01646 221.128
ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [sptrembl;acc:q9bx39] 2968 0.00001 1 0.00001
bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] 757 235.583 1.04968 224.434
baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392] 2500 219.552 1.00275 218.949
bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933] 2185 210.318 1.00663 211.713
bag-family molecular chaperone regulator-2. [swissprot;acc:o95816] 1785 203.874 1.01206 206.332
bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] 459 216.737 1.07748 233.529
bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] 1015 228.906 1.03236 221.73
bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] 651 220.751 1.05877 233.725
band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] 2144 207.864 1.00688 206.443
band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] 2146
band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] 2145 207.862 206.442
bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824] 1567 224.767 1.01646 221.128
barrier-to-autointegration factor (breakpoint cluster region protein 1). [swissprot;acc:o75531] 2804 0.00001 1 0.00001
basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] 933 164.951 1.03635 159.165
basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 2715 215.903 1.00053 216.018
bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061] 2950 0.00001 1 0.00001
bcl-6 interacting corepressor isoform 1. [refseq;acc:nm_017745] 2776
beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457] 1636 199.408 1.01479 202.358
bet3 homolog. [swissprot;acc:o43617] 567 121.261 1.06563 129.219
beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612] 1945 222.151 1.00987 224.343
beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] 2361 208.046 1.00415 207.186
beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 301 166.372 1.10193 150.982
beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884] 2576 213.75 1.00154 213.422
beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425] 2578
beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 50 105 1.26667 133
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 49
beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429] 2222 220.108 1.00637 221.509
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 2221
beta-catenin (pro2286). [swissprot;acc:p35222] 801 214.894 1.04445 224.445
beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] 1510 221.177 1.01795 225.148
beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115] 808 221.785 1.04425 212.386
beta-ureidopropionase (ec 3.5.1.6) (beta-alanine synthase) (n-carbamoyl-beta-alanine amidohydrolase) (bup-1). [swissprot;acc:q9ubr1] 3145 0.00001 1 0.00001
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] 273 267.352 1.10763 241.373
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] 271
bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] 2721 221.116 1.00043 221.022
bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939] 740 235.027 1.0512 223.58
bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] 1848 216.064 1.011 218.441
biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] 1711 215.553 1.01337 218.436

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/