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 measured expected final Hugo
Results: HTML CSV LaTeX Showing element 2408 to 2457 of 3206 in total
Rank
description
measured
expected
final
Hugo
2408 0.184877 0.845209 0.218735248 APIP
2409 0.112482 0.514239 0.218734868 no value
2410 0.0244129 0.111754 0.218452136 VPS8
2411 TRANSCRIPTION FACTOR SMIF; DECAPPING ENZYME HDCP1A. [RefSeq;Acc:NM_018403] 0.289798 1.3266 0.218451681 DCP1A
2412 PUTATIVE N6-DNA-METHYLTRANSFERASE (EC 2.1.1.-) (PROTEIN PRED28) (M.HSAHEMK2P). [SWISSPROT;Acc:Q9Y5N5] 0.357172 1.63578 0.218349656 N6AMT1
2413 0.030828500000000002 0.141189 0.218349163 no value
2414 TUMOR DIFFERENTIALLY EXPRESSED PROTEIN 2. [RefSeq;Acc:NM_178865] 0.0249219 0.114139 0.218346928 SERINC2
2415 TUMOR DIFFERENTIALLY EXPRESSED PROTEIN 1 (TRANSMEMBRANE PROTEIN SBBI99). [SWISSPROT;Acc:Q13530] 0.0298377 0.136653 0.218346469 SERINC3
2416 HOMOLOG OF YEAST MAF1. [RefSeq;Acc:NM_032272] MAF1
2417 TUMOR DIFFERENTIALLY EXPRESSED 1 PROTEIN LIKE. [SWISSPROT;Acc:Q9NRX5] 0.0257797 0.118068 0.218346207 SERINC1
2418 D-3-PHOSPHOGLYCERATE DEHYDROGENASE (EC 1.1.1.95) (3-PGDH). [SWISSPROT;Acc:O43175] 0.489733 2.24292 0.218346174 PHGDH
2419 GENERAL CONTROL OF AMINO ACID SYNTHESIS PROTEIN 5-LIKE 2 (EC 2.3.1.-) (HISTONE ACETYLTRANSFERASE GCN5) (HSGCN5). [SWISSPROT;Acc:Q92830] 0.146069 0.669424 0.218201021 GCN5L2
2420 P300/CBP-ASSOCIATED FACTOR (EC 2.3.1.-) (P/CAF) (HISTONE ACETYLASE PCAF). [SWISSPROT;Acc:Q92831] 0.162045 0.742662 0.218194818 PCAF
2421 FIP1-LIKE 1; REARRANGED IN HYPEREOSINOPHILIA. [RefSeq;Acc:NM_030917] 0.429115 1.96674 0.218185932 FIP1L1
2422 TRANSCRIPTION ELONGATION FACTOR A PROTEIN 2 (TRANSCRIPTION ELONGATION FACTOR S-II PROTEIN 2) (TESTIS-SPECIFIC S-II) (TRANSCRIPTION ELONGATION FACTOR TFIIS.L). [SWISSPROT;Acc:Q15560] 0.0564551 0.258811 0.218132537 TCEA2
2423 TRANSCRIPTION ELONGATION FACTOR A PROTEIN 1 (TRANSCRIPTION ELONGATION FACTOR S-II PROTEIN 1) (TRANSCRIPTION ELONGATION FACTOR TFIIS.O). [SWISSPROT;Acc:P23193] 0.0637011 0.29203 0.218132041 no value
2424 ATP-DEPENDENT DNA HELICASE Q5 (RECQ PROTEIN-LIKE 5) (RECQ5). [SWISSPROT;Acc:O94762] 0.0365106 0.167562 0.217893078 RECQL5
2425 DNA-REPAIR PROTEIN XRCC3 (X-RAY REPAIR CROSS-COMPLEMENTING PROTEIN 3). [SWISSPROT;Acc:O43542] 0.0730211 0.335124 0.21789278 XRCC3
2426 GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE (EC 1.1.1.49) (G6PD). [SWISSPROT;Acc:P11413] 0.146042 0.670248 0.217892482 G6PD
2427 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7 (EC 2.7.1.-) (TRANSFORMING GROWTH FACTOR-BETA-ACTIVATED KINASE 1) (TGF-BETA- ACTIVATED KINASE 1). [SWISSPROT;Acc:O43318] 0.231972 1.06471 0.217873412 MAP3K7
2428 PHOSPHOLIPASE D2 (EC 3.1.4.4) (PLD 2) (CHOLINE PHOSPHATASE 2) (PHOSPHATIDYLCHOLINE-HYDROLYZING PHOSPHOLIPASE D2) (PLD1C) (HPLD2). [SWISSPROT;Acc:O14939] 0.146403 0.672152 0.21781234 PLD2
2429 PHOSPHOLIPASE D1 (EC 3.1.4.4) (PLD 1) (CHOLINE PHOSPHATASE 1) (PHOSPHATIDYLCHOLINE-HYDROLYZING PHOSPHOLIPASE D1) (HPLD1). [SWISSPROT;Acc:Q13393] 0.177815 0.816721 0.217718168 PLD1
2430 SIPL PROTEIN. [RefSeq;Acc:NM_018269] 0.0933761 0.429323 0.217496151 ADI1
2431 FIBULIN-1 PRECURSOR. [SWISSPROT;Acc:P23142] 0.143043 0.657687 0.217494036 FBLN1
2432 0.098396 0.452567 0.217417532 THNSL1
2433 0.192282 0.884993 0.217269515 IMMP1L
2434 IMP2 INNER MITOCHONDRIAL MEMBRANE PROTEASE-LIKE; INNER MITOCHONDRIAL MEMBRANE PEPTIDASE 2 LIKE. [RefSeq;Acc:NM_032549] 0.157677 0.725721 0.217269447 IMMP2L
2435 MICROSOMAL SIGNAL PEPTIDASE 18 KDA SUBUNIT (EC 3.4.-.-) (SPASE 18 KDA SUBUNIT) (SPC18) (ENDOPEPTIDASE SP18). [SWISSPROT;Acc:P21378] no value
2436 0.0346049 0.159272 0.2172692 SETD3
2437 ANAPHASE-PROMOTING COMPLEX SUBUNIT 2; ANAPHASE-PROMOTING COMPLEX 2. [RefSeq;Acc:NM_013366] 0.171257 0.788327 0.217241069 ANAPC2
2438 MY016 PROTEIN. [SPTREMBL;Acc:Q9H3K6] 0.12244 0.563645 0.21722893 BOLA2B
2439 GERANYLGERANYL PYROPHOSPHATE SYNTHETASE (GGPP SYNTHETASE) (GGPPSASE) (GERANYLGERANYL DIPHOSPHATE SYNTHASE) [INCLUDES: DIMETHYLALLYLTRANSFERASE (EC 2.5.1.1); GERANYLTRANSTRANSFERASE (EC 2.5.1.10); FARNESYLTRANSTRANSFERASE (EC 2.5.1.29)]. [SWISSPROT; 0.265861 1.22405 0.217197827 GGPS1
2440 HISTIDYL-TRNA SYNTHETASE (EC 6.1.1.21) (HISTIDINE--TRNA LIGASE) (HISRS). [SWISSPROT;Acc:P12081] 0.507204 2.33574 0.217149169 HARS
2441 MYO-INOSITOL 1-PHOSPHATE SYNTHASE A1. [RefSeq;Acc:NM_016368] 0.0388043 0.178742 0.217096709 no value
2442 UBIQUITIN-LIKE PROTEIN GDX (UBIQUITIN-LIKE PROTEIN 4). [SWISSPROT;Acc:P11441] UBL4A
2443 ARSENICAL PUMP-DRIVING ATPASE (EC 3.6.3.16) (ARSENITE-TRANSLOCATING ATPASE) (ARSENICAL RESISTANCE ATPASE) (ARSENITE-TRANSPORTING ATPASE) (ARSA) (ASNA-I). [SWISSPROT;Acc:O43681] 0.539817 2.48653 0.217096516 no value
2444 0.116413 0.536227 0.217096491 C7orf20
2445 0.0314703 0.14496 0.21709644 UBL4B
2446 LARGE PROLINE-RICH PROTEIN BAT3 (HLA-B-ASSOCIATED TRANSCRIPT 3) (G3). [SWISSPROT;Acc:P46379] 0.109079 0.502445 0.217096399 no value
2447 HISTIDYL-TRNA SYNTHETASE HOMOLOG (EC 6.1.1.21) (HISTIDINE--TRNA LIGASE HOMOLOG) (HISRS). [SWISSPROT;Acc:P49590] 0.443267 2.0418 0.21709619 HARS2
2448 CAAX PRENYL PROTEASE 1 HOMOLOG (EC 3.4.24.-) (PRENYL PROTEIN-SPECIFIC ENDOPROTEASE 1) (FARNESYLATED-PROTEINS CONVERTING ENZYME 1) (FACE-1) (ZINC METALLOPROTEINASE STE24 HOMOLOG). [SWISSPROT;Acc:O75844] 0.205647 0.94731 0.21708522 ZMPSTE24
2449 6-PHOSPHOGLUCONOLACTONASE (EC 3.1.1.31) (6PGL). [SWISSPROT;Acc:O95336] 0.0750119 0.345603 0.217046438 PGLS
2450 0.175357 0.808504 0.216890702 HDHD3
2451 E-1 ENZYME. [RefSeq;Acc:NM_021204] ENOPH1
2452 T-BOX TRANSCRIPTION FACTOR TBX19 (T-BOX PROTEIN 19). [SWISSPROT;Acc:O60806] 0.0222862 0.102768 0.216859334 TBX19
2453 BRACHYURY PROTEIN (T PROTEIN). [SWISSPROT;Acc:O15178] 0.0274799 0.126718 0.216858694 T
2454 0.278378 1.28369 0.216857653 REXO1
2455 REGULATOR OF CHROMOSOME CONDENSATION (CELL CYCLE REGULATORY PROTEIN). [SWISSPROT;Acc:P18754] 0.118612 0.5473 0.21672209 RCC1
2456 TRANSCRIPTION FACTOR 8 (NIL-2-A ZINC FINGER PROTEIN) (NEGATIVE REGULATOR OF IL2). [SWISSPROT;Acc:P37275] 0.0329569 0.15207 0.216721904 ZEB1
2457 ZINC FINGER HOMEOBOX PROTEIN 1B (SMAD INTERACTING PROTEIN 1) (SMADIP1) (HRIHFB2411). [SWISSPROT;Acc:O60315] 0.0271894 0.125458 0.216721134 ZEB2

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/