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.


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 Value Type description 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
Value Type
description
Network Comparison Type
red
green
network_comparison
119 Rooted 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] 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 Measured 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] 5136.78 6895.98 1.34247
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Subtracted 4932.27 7033.29 2101.02
Ranked nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 227.199 192.715 34.484
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Divided 269.278 327.709 1.21699
Squared g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Subtracted 81592.1 56211.1 25381
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Divided 210199 136638 1.53836
Rooted guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Subtracted 40.081 25.1546 14.9264
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Divided 50.3333 62.9942 1.25154
121 Measured jun dimerization protein. [refseq;acc:nm_130469] Subtracted 4932.27 7033.29 2101.02
transcription factor jun-b. [swissprot;acc:p17275] Divided 5579.18 7488.4 1.3422
Ranked cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 269.254 327.655 1.2169
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Subtracted 227.202 192.823 34.379
Squared cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] 81527.6 56190.6 25337
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Divided 199594 130021 1.53509
Rooted homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 50.339 62.9975 1.25147
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] Subtracted 63.6205 48.8838 14.7367
122 Measured fos-related antigen 2. [swissprot;acc:p15408] 4941.95 7037.11 2095.16
high-mobility group 20a. [refseq;acc:nm_018200] Divided 5140.14 6893.53 1.34112
Ranked cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Subtracted 199.949 234.187 34.238
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] Divided 269.248 327.642 1.21688
Squared cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 201896 131906 1.53061
g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Subtracted 81520.8 56188.5 25332.3
Rooted 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] 60.9342 75.1387 14.2045
transcription factor jun-d. [swissprot;acc:p17535] Divided 63.636 79.6225 1.25122
123 Measured cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 24260.3 18172.1 1.33503
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Subtracted 4942.49 7037.32 2094.83
Ranked potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Divided 269.23 327.601 1.21681
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Subtracted 227.032 193.056 33.976
Squared cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] 81478.9 56175.2 25303.7
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Divided 192904 126167 1.52896
Rooted 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] 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
124 Measured fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Subtracted 4944.3 7038.04 2093.74
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Divided 24255.7 18168.9 1.33501
Ranked 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] 208.52 171.595 1.21519
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Subtracted 285.684 252.234 33.45
Squared aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] 71389.9 96037.6 24647.7
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Divided 192779 126095 1.52884
Rooted 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] Subtracted 46.7419 60.9337 14.1918
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Divided 54.6625 67.9477 1.24304
125 Measured hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] 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
Ranked high-mobility group 20a. [refseq;acc:nm_018200] 208.588 171.778 1.21429
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] Subtracted 285.684 252.234 33.45
Squared aquaporin 5. [swissprot;acc:p55064] 71388.5 96035.2 24646.7
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Divided 189976 124480 1.52616
Rooted small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] 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/