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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Gene Rank description Hugo measured final expected
Results: HTML CSV LaTeX Showing element 101 to 150 of 3206 in total
Rank
description
Hugo
measured
final
expected
101 "INOSITOL POLYPHOSPHATE-4-PHOSPHATASE, TYPE II, 105KD; INOSITOL POLYPHOSPHATE 4-PHOSPHATASE II; 4-PHOSPHATASE II. [RefSeq;Acc:NM_003866]" INPP4B 0.046965 0.373794212 0.125644
102 "SELENIDE,WATER DIKINASE 1 (EC 2.7.9.3) (SELENOPHOSPHATE SYNTHETASE 1) (SELENIUM DONOR PROTEIN 1). [SWISSPROT;Acc:P49903]" SEPHS1 0.0620748 0.37379371 0.166067
103 "SELENIDE,WATER DIKINASE 2 (EC 2.7.9.3) (SELENOPHOSPHATE SYNTHETASE 2) (SELENIUM DONOR PROTEIN 2). [SWISSPROT;Acc:Q99611]" SEPHS2 0.0447647 0.373792983 0.119758
104 FLAVOPROTEIN OXIDOREDUCTASE MICAL2. [RefSeq;Acc:NM_014632] MICAL2 0.42874 0.373792502 1.147
105 VAV-2 PROTEIN. [SWISSPROT;Acc:P52735] VAV2 0.433722 0.371668266 1.16696
106 WISKOTT-ALDRICH SYNDROME PROTEIN INTERACTING PROTEIN (WASP INTERACTING PROTEIN) (PRPL-2 PROTEIN). [SWISSPROT;Acc:O43516] WIPF1 0.23886 0.367534598 0.649898
107 SEQUESTOSOME 1; UBIQUITIN-BINDING PROTEIN P62; PHOSPHOTYROSINE INDEPENDENT LIGAND FOR THE LCK SH2 DOMAIN P62. [RefSeq;Acc:NM_003900] SQSTM1 0.0692099 0.366704109 0.188735
108 "NONSPECIFIC LIPID-TRANSFER PROTEIN, MITOCHONDRIAL PRECURSOR (NSL-TP) (STEROL CARRIER PROTEIN 2) (SCP-2) (STEROL CARRIER PROTEIN X) (SCP-X) (SCPX). [SWISSPROT;Acc:P22307]" SCP2 0.192957 0.366703155 0.526194
109 VINEXIN (SH3-CONTAINING ADAPTOR MOLECULE-1) (SCAM-1). [SWISSPROT;Acc:O60504] SORBS3 0.619368 0.362780563 1.70728
110 DNA POLYMERASE EPSILON SUBUNIT B (EC 2.7.7.7) (DNA POLYMERASE II SUBUNIT B). [SWISSPROT;Acc:P56282] POLE2 0.0886771 0.362746871 0.24446
111 NUCLEOLYSIN TIA-1 (RNA-BINDING PROTEIN TIA-1) (P40-TIA-1) [CONTAINS: P15-TIA-1]. [SWISSPROT;Acc:P31483] TIA1 0.401253 0.361525016 1.10989
112 C11orf56 0.0828978 0.361306491 0.229439
113 "SWI/SNF-RELATED, MATRIX-ASSOCIATED, ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY F MEMBER 1 (SWI-SNF COMPLEX PROTEIN P270) (B120). [SWISSPROT;Acc:O14497]" ARID1A 0.182783 0.361164845 0.506093
114 PROGRAMMED CELL DEATH PROTEIN 6 (PROBABLE CALCIUM-BINDING PROTEIN ALG- 2). [SWISSPROT;Acc:O75340] PDCD6
115 BRG1-BINDING PROTEIN ELD/OSA1; ELD (EYELID)/OSA PROTEIN. [RefSeq;Acc:NM_020732] ARID1B 0.155731 0.36115221 0.431206
116 SORCIN (22 KDA PROTEIN) (CP-22) (V19). [SWISSPROT;Acc:P30626] SRI 0.137538 0.361138098 0.380846
117 GRANCALCIN. [SWISSPROT;Acc:P28676] GCA 0.135756 0.361137713 0.375912
118 "CALCIUM-DEPENDENT PROTEASE, SMALL SUBUNIT (CALPAIN REGULATORY SUBUNIT) (CALCIUM-ACTIVATED NEUTRAL PROTEINASE) (CANP). [SWISSPROT;Acc:P04632]" CAPNS1 0.133134 0.361134394 0.368655
119 NUCLEOLYSIN TIAR (TIA-1 RELATED PROTEIN). [SWISSPROT;Acc:Q01085] TIAL1 0.374769 0.361111753 1.03782
120 PONSIN; SH3-DOMAIN PROTEIN 5 (PONSIN). [RefSeq;Acc:NM_015385] SORBS1 0.795875 0.36063193 2.20689
121 ARG/ABL-INTERACTING PROTEIN 2 ISOFORM 2; ARG BINDING PROTEIN 2. [RefSeq;Acc:NM_021069] SORBS2 0.864436 0.360318287 2.39909
122 SON OF SEVENLESS PROTEIN HOMOLOG 2 (SOS-2). [SWISSPROT;Acc:Q07890] SOS2 0.342509 0.358540793 0.955286
123 SMALL NUCLEAR RIBONUCLEOPROTEIN SM D1 (SNRNP CORE PROTEIN D1) (SM-D1) (SM-D AUTOANTIGEN). [SWISSPROT;Acc:P13641] SNRPD1 0.36177 0.358202305 1.00996
124 SON OF SEVENLESS PROTEIN HOMOLOG 1 (SOS-1). [SWISSPROT;Acc:Q07889] SOS1 0.393069 0.357647583 1.09904
125 C9orf41 0.557991 0.357121097 1.56247
126 UBA/UBX 33.3 KDA PROTEIN. [SWISSPROT;Acc:Q04323] no value 0.375086 0.3550505 1.05643
127 ERO1-LIKE. [RefSeq;Acc:NM_014584] 0.0588477 0.355049624 0.165745
128 HOMEOBOX PROTEIN HOX-A10 (HOX-1H) (HOX-1.8) (PL). [SWISSPROT;Acc:P31260] HOXA10 0.911869 0.351521939 2.59406
129 DELTEX 2. [RefSeq;Acc:NM_020892] DTX2 0.162688 0.351513868 0.462821
130 HOMEOBOX PROTEIN HOX-B9 (HOX-2E) (HOX-2.5). [SWISSPROT;Acc:P17482] HOXB9 1.00641 0.351459043 2.86352
131 HOMEOBOX PROTEIN HOX-A9 (HOX-1G). [SWISSPROT;Acc:P31269] HOXA9 1.02451 0.35144935 2.9151
132 HOMEOBOX PROTEIN HOX-C9 (HOX-3B). [SWISSPROT;Acc:P31274] HOXC9 1.0305 0.351424625 2.93235
133 GAMMA-AMINOBUTYRIC-ACID RECEPTOR GAMMA-3 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:Q99928] GABRG3 0.290469 0.351386401 0.826637
134 INTERLEUKIN-1 RECEPTOR-ASSOCIATED KINASE 4; INTERLEUKIN-1 RECEPTOR ASSOCIATED KINASE 4. [RefSeq;Acc:NM_016123] no value
135 FORKHEAD BOX PROTEIN G1C (FORKHEAD-RELATED PROTEIN FKHL3) (HFK3) (FRAGMENT). [SWISSPROT;Acc:Q14488] FOXG1
136 PHOSPHATIDYLSERINE RECEPTOR; PHOSPHATIDYLSERINE RECEPTOR BETA. [RefSeq;Acc:NM_015167] JMJD6
137 GAMMA-AMINOBUTYRIC-ACID RECEPTOR GAMMA-2 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P18507] GABRG2 0.250789 0.351383388 0.713719
138 GAMMA-AMINOBUTYRIC-ACID RECEPTOR GAMMA-1 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:Q8N1C3] GABRG1 0.248966 0.351383355 0.708531
139 GAMMA-AMINOBUTYRIC-ACID RECEPTOR EPSILON SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P78334] GABRE 0.219446 0.351382337 0.624522
140 GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-4 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P48169] GABRA4 0.217015 0.351382115 0.617604
141 GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-3 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P34903] GABRA3 0.2125 0.351381965 0.604755
142 GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-6 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:Q16445] GABRA6 0.218317 0.351381758 0.62131
143 GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-1 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P14867] GABRA1 0.211371 0.351381364 0.601543
144 GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-2 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P47869] GABRA2 0.211718 0.351380508 0.602532
145 SIMILAR TO EXPRESSED SEQUENCE AA415817. [SPTREMBL;Acc:Q8N4Q9] PDXDC1 0.306813 0.351374287 0.87318
146 NADH-UBIQUINONE OXIDOREDUCTASE B14 SUBUNIT (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-B14) (CI-B14). [SWISSPROT;Acc:P56556] NDUFA6 0.0694539 0.351373543 0.197664
147 DELTEX HOMOLOG 1; HDX-1. [RefSeq;Acc:NM_004416] DTX1 0.177901 0.351313617 0.506388
148 FKBP15 0.474383 0.351267318 1.35049
149 "KH DOMAIN CONTAINING, RNA BINDING, SIGNAL TRANSDUCTION ASSOCIATED 3; SAM68-LIKE PHOSPHOTYROSINE PROTEIN, T-STAR. [RefSeq;Acc:NM_006558]" KHDRBS3 0.230683 0.351266984 0.656717
150 "KH DOMAIN CONTAINING, RNA BINDING, SIGNAL TRANSDUCTION ASSOCIATED 1; GAP-ASSOCIATED TYROSINE PHOSPHOPROTEIN P62 (SAM68). [RefSeq;Acc:NM_006559]" KHDRBS1 0.176025 0.351266675 0.501115

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
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/