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 951 to 1000 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
119 serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] Rooted Subtracted 63.6507 48.7127 14.938
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Divided 50.3247 62.9892 1.25166
120 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Squared Subtracted 81592.1 56211.1 25381
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Rooted 40.081 25.1546 14.9264
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Measured Divided 5136.78 6895.98 1.34247
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Rooted 50.3333 62.9942 1.25154
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Ranked Subtracted 227.199 192.715 34.484
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Squared Divided 210199 136638 1.53836
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Ranked 269.278 327.709 1.21699
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Measured Subtracted 4932.27 7033.29 2101.02
121 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Squared 81527.6 56190.6 25337
cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Ranked Divided 269.254 327.655 1.2169
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Rooted 50.339 62.9975 1.25147
jun dimerization protein. [refseq;acc:nm_130469] Measured Subtracted 4932.27 7033.29 2101.02
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Ranked 227.202 192.823 34.379
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Rooted 63.6205 48.8838 14.7367
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Squared Divided 199594 130021 1.53509
transcription factor jun-b. [swissprot;acc:p17275] Measured 5579.18 7488.4 1.3422
122 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Squared 201896 131906 1.53061
cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Ranked Subtracted 199.949 234.187 34.238
fos-related antigen 2. [swissprot;acc:p15408] Measured 4941.95 7037.11 2095.16
g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Squared 81520.8 56188.5 25332.3
high-mobility group 20a. [refseq;acc:nm_018200] Measured Divided 5140.14 6893.53 1.34112
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Rooted Subtracted 60.9342 75.1387 14.2045
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Ranked Divided 269.248 327.642 1.21688
transcription factor jun-d. [swissprot;acc:p17535] Rooted 63.636 79.6225 1.25122
123 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Squared Subtracted 81478.9 56175.2 25303.7
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Measured Divided 24260.3 18172.1 1.33503
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] Rooted Subtracted 46.7419 60.9337 14.1918
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Divided 54.6527 67.9743 1.24375
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Ranked 269.23 327.601 1.21681
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Measured Subtracted 4942.49 7037.32 2094.83
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Squared Divided 192904 126167 1.52896
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Ranked Subtracted 227.032 193.056 33.976
124 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Squared 71389.9 96037.6 24647.7
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] Rooted 46.7419 60.9337 14.1918
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Measured 4944.3 7038.04 2093.74
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Ranked Divided 208.52 171.595 1.21519
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Measured 24255.7 18168.9 1.33501
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Rooted 54.6625 67.9477 1.24304
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Ranked Subtracted 285.684 252.234 33.45
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Squared Divided 192779 126095 1.52884
125 aquaporin 5. [swissprot;acc:p55064] Subtracted 71388.5 96035.2 24646.7
high-mobility group 20a. [refseq;acc:nm_018200] Ranked Divided 208.588 171.778 1.21429
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Measured Subtracted 12471.7 14561.7 2090
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Divided 24255.7 18168.9 1.33501
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Squared 189976 124480 1.52616
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Ranked Subtracted 285.684 252.234 33.45
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Rooted Divided 54.8203 67.934 1.23921
son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Subtracted 35.6294 49.8119 14.1825

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/