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 [...,...].
Value Type Gene Interaction Map Rank Filtered Network Comparison Type description green red network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 29840 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
Filtered
Network Comparison Type
description
green
red
network_comparison
126 0 Divided calcyphosine. [swissprot;acc:q13938] 635.875 472.524 1.3457
Subtracted pp3111 protein. [refseq;acc:nm_022156] 530 789 259
1 Divided cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 18164.9 24250 1.33499
Subtracted rad50-interacting protein 1. [refseq;acc:nm_021930] 2394.5 450.5 1944
127 0 Divided lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] 64 86 1.34375
Subtracted alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] 1759.22 2017.91 258.69
1 Divided transcription factor jun-d. [swissprot;acc:p17535] 7523.39 5638.2 1.33436
Subtracted rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 2394.5 450.5 1944
128 0 Divided mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] 60.8613 81.504 1.33918
Subtracted importin 9. [refseq;acc:nm_018085] 1397.66 1143.55 254.11
1 Divided luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 5810.82 4355.61 1.3341
Subtracted t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] 12944.2 11004.2 1940
129 0 Divided protein hspc134 (protein cda04). [swissprot;acc:q9by43] 454.837 606.485 1.33341
Subtracted nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] 1397.66 1143.55 254.11
1 Divided luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 5811.49 4358.13 1.33348
Subtracted protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] 13346.9 15274.9 1928
130 0 Divided maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] 56 42 1.33333
Subtracted chromodomain y-like protein 2. [refseq;acc:nm_152342] 2799.81 3053.31 253.5
1 Divided forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 2978.53 2234.68 1.33287
Subtracted p66 alpha. [refseq;acc:nm_017660] 10911.1 12839 1927.9
131 0 Divided serpin b11. [swissprot;acc:q96p15] 56 42 1.33333
Subtracted protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] 4658.69 4912.01 253.32
1 Divided forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 2978.57 2234.73 1.33285
Subtracted transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] 10911.1 12839 1927.9
132 0 Divided cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] 56 42 1.33333
Subtracted voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 2202 1949.36 252.64
1 Divided forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 2980.35 2236.61 1.33253
Subtracted tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] 10911.1 12839 1927.9
133 0 Divided 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] 335 252 1.32937
Subtracted testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] 2784.59 3036.85 252.26
1 Divided gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 17580.4 23421.5 1.33225
Subtracted cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 10887.2 12798.9 1911.7
134 0 Divided mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] 346.751 260.986 1.32862
Subtracted testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] 2784.08 3036.29 252.21
1 Divided gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 16426.1 21785.2 1.32626
Subtracted g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] 10886 12796.8 1910.8
135 0 Divided rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] 613.614 814.485 1.32736
Subtracted 60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] 476.619 728.65 252.031
1 Divided apg3p; pc3-96 protein. [refseq;acc:nm_022488] 16426.1 21785.2 1.32626
Subtracted transcription factor jun-b. [swissprot;acc:p17275] 7488.4 5579.18 1909.22
136 0 Divided transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 1150.51 1526.38 1.3267
Subtracted glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] 1152.06 903.767 248.293
1 Divided 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] 4763.34 3620.77 1.31556
Subtracted cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] 10880.5 12787.6 1907.1
137 0 Divided heat shock factor binding protein 1. [swissprot;acc:o75506] 1233.41 1631.18 1.3225
Subtracted ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 7276.12 7520.78 244.66
1 Divided 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] 4763.34 3620.77 1.31556
Subtracted g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] 10879.9 12786.6 1906.7
138 0 Divided 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] 154.804 204.382 1.32026
Subtracted 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 1906.28 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/