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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Value Type Interaction Map Gene Rank green description Network Comparison Type Filtered red network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 77072 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
green
description
Network Comparison Type
Filtered
red
network_comparison
126 530 pp3111 protein. [refseq;acc:nm_022156] Subtracted 0 789 259
635.875 calcyphosine. [swissprot;acc:q13938] Divided 472.524 1.3457
2394.5 rad50-interacting protein 1. [refseq;acc:nm_021930] Subtracted 1 450.5 1944
18164.9 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Divided 24250 1.33499
127 64 lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] 0 86 1.34375
1759.22 alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] Subtracted 2017.91 258.69
2394.5 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1 450.5 1944
7523.39 transcription factor jun-d. [swissprot;acc:p17535] Divided 5638.2 1.33436
128 60.8613 mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] 0 81.504 1.33918
1397.66 importin 9. [refseq;acc:nm_018085] Subtracted 1143.55 254.11
5810.82 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Divided 1 4355.61 1.3341
12944.2 t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Subtracted 11004.2 1940
129 454.837 protein hspc134 (protein cda04). [swissprot;acc:q9by43] Divided 0 606.485 1.33341
1397.66 nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] Subtracted 1143.55 254.11
5811.49 luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Divided 1 4358.13 1.33348
13346.9 protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Subtracted 15274.9 1928
130 56 maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Divided 0 42 1.33333
2799.81 chromodomain y-like protein 2. [refseq;acc:nm_152342] Subtracted 3053.31 253.5
2978.53 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Divided 1 2234.68 1.33287
10911.1 p66 alpha. [refseq;acc:nm_017660] Subtracted 12839 1927.9
131 56 serpin b11. [swissprot;acc:q96p15] Divided 0 42 1.33333
2978.57 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 1 2234.73 1.33285
4658.69 protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Subtracted 0 4912.01 253.32
10911.1 transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] 1 12839 1927.9
132 56 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] Divided 0 42 1.33333
2202 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Subtracted 1949.36 252.64
2980.35 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Divided 1 2236.61 1.33253
10911.1 tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Subtracted 12839 1927.9
133 335 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] Divided 0 252 1.32937
2784.59 testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] Subtracted 3036.85 252.26
10887.2 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 1 12798.9 1911.7
17580.4 gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Divided 23421.5 1.33225
134 346.751 mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] 0 260.986 1.32862
2784.08 testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Subtracted 3036.29 252.21
10886 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] 1 12796.8 1910.8
16426.1 gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Divided 21785.2 1.32626
135 476.619 60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] Subtracted 0 728.65 252.031
613.614 rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] Divided 814.485 1.32736
7488.4 transcription factor jun-b. [swissprot;acc:p17275] Subtracted 1 5579.18 1909.22
16426.1 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Divided 21785.2 1.32626
136 1150.51 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 0 1526.38 1.3267
1152.06 glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Subtracted 903.767 248.293
4763.34 nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Divided 1 3620.77 1.31556
10880.5 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Subtracted 12787.6 1907.1
137 1233.41 heat shock factor binding protein 1. [swissprot;acc:o75506] Divided 0 1631.18 1.3225
4763.34 ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] 1 3620.77 1.31556
7276.12 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Subtracted 0 7520.78 244.66
10879.9 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] 1 12786.6 1906.7
138 154.804 ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] Divided 0 204.382 1.32026
1906.28 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Subtracted 1663.73 242.55

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/