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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2530 to 2579 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1265 dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135] Divided 5894.47 6383.73 1.083
1266 mitotic checkpoint protein bub3. [swissprot;acc:o43684] Subtracted 5470.44 5949.49 479.05
sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691] Divided 5894.47 6383.73 1.083
1267 cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850]
zinc finger protein 207. [swissprot;acc:o43670] Subtracted 5470.44 5949.49 479.05
1268 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] 4250.18 4729.12 478.94
sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137] Divided 5894.47 6383.73 1.083
1269 peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] Subtracted 7048.79 7527.42 478.63
xap-5 protein (hxc-26 protein). [swissprot;acc:q14320] Divided 5894.47 6383.73 1.083
1270 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Subtracted 5654.53 6132.76 478.23
epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [refseq;acc:nm_022772] Divided 5685.08 6156.48 1.08292
1271 mitotic checkpoint serine/threonine-protein kinase bub1 beta (ec 2.7.1.-) (hbubr1) (mad3/bub1-related protein kinase) (mitotic checkpoint kinase mad3l). [swissprot;acc:o60566] 5528.65 5985.58 1.08265
retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] Subtracted 5654.54 6132.69 478.15
1272 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Divided 5528.65 5985.58 1.08265
rad54-like protein; rad54 homolog. [refseq;acc:nm_003579] Subtracted 5754.84 6232.83 477.99
1273 phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] Divided 5885 6371.14 1.08261
proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818] Subtracted 6216.12 6693.38 477.26
1274 3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405] Divided 5885 6371.14 1.08261
megf6 (fragment). [sptrembl;acc:o75095] Subtracted 5980.41 6457.51 477.1
1275 3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213] Divided 5885 6371.14 1.08261
proteasome subunit alpha type 7-like (ec 3.4.25.1). [swissprot;acc:q8taa3] Subtracted 6216.13 6693.13 477
1276 6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [swissprot;acc:p52209] 5988.06 6464.94 476.88
peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] Divided 6437.99 6969.67 1.08258
1277 heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652]
serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] Subtracted 5418.33 5895.2 476.87
1278 eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] 4131.04 4607.9 476.86
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Divided 6437.99 6969.67 1.08258
1279 eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Subtracted 4131.04 4607.9 476.86
heat shock cognate 71 kda protein. [swissprot;acc:p11142] Divided 6437.99 6969.67 1.08258
1280 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Subtracted 6036.22 6512.64 476.42
dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887] Divided 6350.81 6874.88 1.08252
1281 dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561] Subtracted 5322.16 5798.38 476.22
orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736] Divided 6230.49 6744.5 1.0825
1282 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] Subtracted 5322.16 5798.38 476.22
nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570] Divided 6230.38 6744.35 1.08249
1283 adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235] Subtracted 5322.16 5798.38 476.22
orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [swissprot;acc:p43354] Divided 6229.16 6742.79 1.08246
1284 mitogen-activated protein kinase 3 (ec 2.7.1.37) (extracellular signal-regulated kinase 1) (erk-1) (insulin-stimulated map2 kinase) (map kinase 1) (mapk 1) (p44-erk1) (ert2) (p44-mapk) (microtubule- associated protein-2 kinase). [swissprot;acc:p27361] Subtracted 6079.85 6556.07 476.22
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Divided 6413.32 6941.48 1.08235
1285 adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141] Subtracted 5322.16 5798.38 476.22
cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4] Divided 6207.57 6718.7 1.08234
1286 casein kinase i alpha s-like. [refseq;acc:nm_145203] Subtracted 4906.33 5382.5 476.17
cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] Divided 5655.85 6120.64 1.08218
1287 casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] Subtracted 4906.33 5382.5 476.17
cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] Divided 5655.85 6120.64 1.08218
1288 chromodomain y-like protein 2. [refseq;acc:nm_152342] Subtracted 7101.7 7577.75 476.05
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Divided 5655.85 6120.64 1.08218
1289 likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033]
ribosomal protein s6 kinase alpha 3 (ec 2.7.1.37) (s6k-alpha 3) (90 kda ribosomal protein s6 kinase 3) (p90-rsk 3) (ribosomal s6 kinase 2) (rsk-2) (pp90rsk2) (insulin-stimulated protein kinase 1) (ispk-1). [swissprot;acc:p51812] Subtracted 6079.45 6555.4 475.95
1290 calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [swissprot;acc:q13555]

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/