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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1280 to 1329 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
320 Rooted 40s ribosomal protein s29. [swissprot;acc:p30054] 50.2784 45.294 1.11005
321 Measured ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] 20911 24908.5 1.19117
Ranked c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 241.892 265.959 1.09949
Squared putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] 33526 42390.2 1.2644
Rooted u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] 55.9231 62.0565 1.10968
322 Measured anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 20911 24908.5 1.19117
Ranked deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 86.7483 78.8995 1.09948
Squared nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] 33522.8 42384.8 1.26436
Rooted rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] 60.594 67.2244 1.10942
323 Measured u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] 4620.76 5501.94 1.1907
Ranked 60s ribosomal protein l23a. [swissprot;acc:p29316] 241.884 265.945 1.09947
Squared nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] 33514.4 42370.8 1.26426
Rooted cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] 50.3803 45.4193 1.10923
324 Measured deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 28136.5 33457.6 1.18912
Ranked 40s ribosomal protein s23. [swissprot;acc:p39028] 243.944 268.195 1.09941
Squared histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] 34527.9 43507.9 1.26008
Rooted fad synthetase. [refseq;acc:nm_025207] 50.3803 45.4193 1.10923
325 Measured septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] 16177.9 19235.4 1.18899
Ranked 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] 243.944 268.195 1.09941
Squared histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] 34506.3 43476 1.25994
Rooted 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] 50.3803 45.4193 1.10923
326 Measured atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 3432.96 4081.21 1.18883
Ranked 60s ribosomal protein l5. [swissprot;acc:p46777] 241.899 265.924 1.09932
Squared anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] 69124.3 54897.4 1.25915
Rooted ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] 50.3803 45.4193 1.10923
327 Measured septin 10 isoform 1. [refseq;acc:nm_144710] 16067.4 19094.4 1.18839
Ranked dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] 243.817 267.962 1.09903
Squared luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 16424.1 20645.8 1.25704
Rooted 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] 50.3803 45.4193 1.10923
328 Measured brain protein 44. [swissprot;acc:o95563] 15999.1 19007.1 1.18801
Ranked atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 258.437 235.183 1.09888
Squared luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 16442.8 20662.7 1.25664
Rooted nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] 50.3803 45.4193 1.10923
329 Measured septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] 15999.1 19007.1 1.18801
Ranked neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] 312 284 1.09859
Squared metaxin 2. [swissprot;acc:o75431] 41236 51807 1.25635
Rooted cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] 50.3803 45.4193 1.10923
330 Measured septin 6. [swissprot;acc:q14141] 15959.9 18957.1 1.1878
Ranked chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] 312 284 1.09859
Squared huntingtin interacting protein c. [refseq;acc:nm_012272] 16203.4 20339.9 1.25529
Rooted 60s ribosomal protein l32. [swissprot;acc:p02433] 50.519 45.5497 1.1091
331 Measured pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 20287.2 17083.8 1.18751
Ranked doc-1 related protein (doc-1r). [swissprot;acc:o75956] 312 284 1.09859
Squared ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 33100.3 41520.6 1.25439
Rooted apical-like protein (apxl protein). [swissprot;acc:q13796] 60.6697 67.2802 1.10896
332 Measured pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 5051.16 5975.51 1.183
Ranked neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] 312 284 1.09859
Squared nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] 14464.3 18142.8 1.25432
Rooted shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] 60.6732 67.2827 1.10894
333 Measured nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] 5039.63 5961.83 1.18299

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/